RecentChanges
clonotypeR
http://clonotyper.branchable.com/recentchanges/
clonotypeR
ikiwiki
2017-06-07T02:02:45Z
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_008f6f80dda6a844e7d9e92121af25e737a3a3ac/
plessy
2017-06-07T02:02:45Z
2017-06-07T02:02:45Z
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Merge branch 'master' of ssh://clonotyper.branchable.com<br />
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change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_3f109586a2d8c4e0b70c3cd74957fc795094ce4d/
plessy
2017-06-07T02:01:13Z
2017-06-07T02:01:13Z
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<div class="changelog">
Announce support of SAMtools version 1.3 or higher.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 717f931..5694454 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -51,6 +51,7 @@ See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a
### Recent news
+ * June 2017: Minor update to support the use of SAMtools version 1.3 or higher.
* October 2015: Application note preprint deposited in [bioRxiv](http://biorxiv.org/content/early/2015/10/08/028696).
* October 2014: New stable version [1.4](http://www.bioconductor.org/packages/3.0/bioc/html/clonotypeR.html)
released on Bioconductor.
</pre>
</div>
change to scripts/clonotypeR on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_017e857fca18c6888ee31c8800d518b7503f6058/
plessy
2017-06-07T01:59:38Z
2017-06-07T01:59:38Z
<div id="change-017e857fca18c6888ee31c8800d518b7503f6058" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=scripts/clonotypeR;h=7c7055f0c0466889cd34720b06a1602a7df8e62a;hp=a6553256e0d169f0320d0ab8d98e9736ba9208a7;hb=017e857fca18c6888ee31c8800d518b7503f6058;hpb=42f0eb22971c4c4f9af095b6502262342915e444" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=scripts%2FclonotypeR" rel="nofollow">scripts/clonotypeR</a>
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<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=plessy" rel="nofollow">plessy</a>
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<span class="desc"><br />Commit type:</span>
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<span class="changedate"><time datetime="2017-06-07T01:59:38Z" class="relativedate" title="Wed, 07 Jun 2017 01:59:38 +0000">01:59:38 06/07/17</time></span>
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</span>
</div>
<div class="changelog">
Support the use of older and newer versions of SAMtools.<br />
</div>
<div class="diff">
<pre>
diff --git a/scripts/clonotypeR b/scripts/clonotypeR
index a655325..7c7055f 100755
--- a/scripts/clonotypeR
+++ b/scripts/clonotypeR
@@ -52,6 +52,19 @@ function test_extract_dir {
fi
}
+# There was a backward-incompatible change of syntax for "samtools sort" in version 1.3.
+# https://github.com/samtools/samtools/blob/develop/NEWS
+function samtools_sort {
+ samtools 2>&1 | grep Version | grep -q htslib
+ if [ $? -ne 0 ]
+ then
+ printf "Your samtools version is old; consider upgrading\n"
+ samtools sort - $1
+ else
+ samtools sort - -o $1.bam
+ fi
+}
+
case $1 in
detect)
shift
@@ -62,7 +75,7 @@ case $1 in
LIBRARY=$(basename $FASTQ_FILE .fastq)
bwa bwasw -t${THREADS:-1} $CLONOTYPER_REFERENCE/V-C/index $FASTQ_FILE |
samtools view -Su - |
- samtools sort - $EXTRACT_DIR/$LIBRARY
+ samtools_sort $EXTRACT_DIR/$LIBRARY
samtools index $EXTRACT_DIR/$LIBRARY.bam
done
;;
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_ea0c992ea70b3d947a190e4ffff17791bcc93d7b/
https://launchpad.net/~plessy
2017-01-12T05:01:23Z
2017-01-12T05:01:23Z
<div id="change-ea0c992ea70b3d947a190e4ffff17791bcc93d7b" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
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<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2017-01-12T05:01:23Z" class="relativedate" title="Thu, 12 Jan 2017 05:01:23 +0000">05:01:23 01/12/17</time></span>
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</span>
</div>
<div class="changelog">
Link to TraCeR, https://github.com/Teichlab/tracer<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 70612c6..a26f91b 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -42,6 +42,7 @@ to try alternative solutions, you can have a look at
[MiXCR](https://milaboratory.com/software/mixcr/),
[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
[tcR](https://imminfo.github.io/tcr/),
+[TraCeR](https://github.com/Teichlab/tracer),
[VDJviz](https://github.com/antigenomics/vdjviz), or
[VDJtools](https://github.com/mikessh/vdjtools).
See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_dc0edb60eb6101c13e9951e1bfc017e8853dfd18/
https://launchpad.net/~plessy
2016-11-04T00:38:50Z
2016-11-04T00:38:50Z
<div id="change-dc0edb60eb6101c13e9951e1bfc017e8853dfd18" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<span class="committype">web</span>
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<span class="changedate"><time datetime="2016-11-04T00:38:50Z" class="relativedate" title="Fri, 04 Nov 2016 00:38:50 +0000">00:38:50 11/04/16</time></span>
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</span>
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<div class="changelog">
MiXCR<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 717f931..70612c6 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -39,6 +39,7 @@ to try alternative solutions, you can have a look at
[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
[MiTCR](http://mitcr.milaboratory.com/),
[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
+[MiXCR](https://milaboratory.com/software/mixcr/),
[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
[tcR](https://imminfo.github.io/tcr/),
[VDJviz](https://github.com/antigenomics/vdjviz), or
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_02185d3e4c2fa02665796ada19d6ff3545c49a0a/
https://launchpad.net/~plessy
2016-06-23T02:11:00Z
2016-06-23T02:11:00Z
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<span class="desc"><br />Changed pages:</span>
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<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-06-23T02:11:00Z" class="relativedate" title="Thu, 23 Jun 2016 02:11:00 +0000">02:11:00 06/23/16</time></span>
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</span>
</div>
<div class="changelog">
Link to tcR.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 293d9aa..717f931 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -40,6 +40,7 @@ to try alternative solutions, you can have a look at
[MiTCR](http://mitcr.milaboratory.com/),
[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
+[tcR](https://imminfo.github.io/tcr/),
[VDJviz](https://github.com/antigenomics/vdjviz), or
[VDJtools](https://github.com/mikessh/vdjtools).
See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_0cb87d17eef2b8d78ce222e2fc58ddd8f381eb9c/
https://launchpad.net/~plessy
2016-06-16T07:10:38Z
2016-06-16T07:10:38Z
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<span class="desc"><br />Changed pages:</span>
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</span>
<span class="desc"><br />Changed by:</span>
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<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-06-16T07:10:38Z" class="relativedate" title="Thu, 16 Jun 2016 07:10:38 +0000">07:10:38 06/16/16</time></span>
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</span>
</div>
<div class="changelog">
VDJviz<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 4745394..293d9aa 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -39,7 +39,8 @@ to try alternative solutions, you can have a look at
[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
[MiTCR](http://mitcr.milaboratory.com/),
[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
-[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full), or
+[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
+[VDJviz](https://github.com/antigenomics/vdjviz), or
[VDJtools](https://github.com/mikessh/vdjtools).
See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_7fea58505e42b958dbc6c8aec4f5ea0955f21265/
d.tenenbaum
2016-05-15T20:14:22Z
2016-05-15T20:14:22Z
<div id="change-7fea58505e42b958dbc6c8aec4f5ea0955f21265" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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</span>
<span class="desc"><br />Changed by:</span>
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-05-15T20:14:22Z" class="relativedate" title="Sun, 15 May 2016 20:14:22 +0000">20:14:22 05/15/16</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Version bump to trigger package rebuilding now that purl()'ing issue<br />
has been correctly identified. knitr does not create purl()'ed<br />
(Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which<br />
the build system was setting. Now it's not set, so these .R files are<br />
now created. See https://github.com/yihui/knitr/issues/1212 for more.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@117512 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 34c27ab..eb10cc0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.11.1
+Version: 1.11.2
Date: 2016-04-23
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_44838833797ace350e607caed97513773e946db0/
d.tenenbaum
2016-05-11T23:05:31Z
2016-05-11T23:05:31Z
<div id="change-44838833797ace350e607caed97513773e946db0" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="desc"><br />Changed by:</span>
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<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-05-11T23:05:31Z" class="relativedate" title="Wed, 11 May 2016 23:05:31 +0000">23:05:31 05/11/16</time></span>
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</span>
</div>
<div class="changelog">
Bump version of all packages that use knitr for vignettes.<br />
This is because of an issue (now fixed) in knitr which failed to<br />
create purl()'ed R files from vignette sources and include them in the<br />
package. This version bump will cause these packages to propagate<br />
with those R files included.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@117323 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 31dd866..34c27ab 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.11.0
+Version: 1.11.1
Date: 2016-04-23
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_24ae6522a3957309b5c61ea3b6214d973a3eeee4/
d.tenenbaum
2016-05-03T21:30:44Z
2016-05-03T21:30:44Z
<div id="change-24ae6522a3957309b5c61ea3b6214d973a3eeee4" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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</span>
<span class="desc"><br />Changed by:</span>
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</span>
</div>
<div class="changelog">
bump version after creating 3.3 branch<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@117081 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 27b25a2..31dd866 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.10.0
+Version: 1.11.0
Date: 2016-04-23
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5c0b4ef50124e1acdd58b23587a77905e1964ea6/
d.tenenbaum
2016-05-03T21:20:18Z
2016-05-03T21:20:18Z
<div id="change-5c0b4ef50124e1acdd58b23587a77905e1964ea6" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=27b25a280a309b0fa104daadc0f3ec0aed3f2436;hp=2f4b79c3651005f63657b9af0de16a1b9e6b8311;hb=5c0b4ef50124e1acdd58b23587a77905e1964ea6;hpb=10cebe75d08728ad393b2fc93dbcf347ef089e3f" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
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</span>
</div>
<div class="changelog">
Bump versions prior to creation of 3.3 branch<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@117079 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 2f4b79c..27b25a2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.9.1
+Version: 1.10.0
Date: 2016-04-23
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to ChangeLog DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_10cebe75d08728ad393b2fc93dbcf347ef089e3f/
c.plessy
2016-04-23T07:02:19Z
2016-04-23T07:02:19Z
<div id="change-10cebe75d08728ad393b2fc93dbcf347ef089e3f" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=ChangeLog;h=460527f0375f54a0b118c24d44fbf0f22868af2b;hp=3fad6518bb98ed2b28bb513f4340cf016279b0c1;hb=10cebe75d08728ad393b2fc93dbcf347ef089e3f;hpb=41c084d4850a27dc41076905be69fcecdd9f4923" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=ChangeLog" rel="nofollow">ChangeLog</a>
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=2f4b79c3651005f63657b9af0de16a1b9e6b8311;hp=1d65d568b17247fc862f2c50eb53dce2d2797188;hb=10cebe75d08728ad393b2fc93dbcf347ef089e3f;hpb=41c084d4850a27dc41076905be69fcecdd9f4923" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-04-23T07:02:19Z" class="relativedate" title="Sat, 23 Apr 2016 07:02:19 +0000">07:02:19 04/23/16</time></span>
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</span>
</div>
<div class="changelog">
Increment minor version number to trigger update.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@116714 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/ChangeLog b/ChangeLog
index 3fad651..460527f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,6 @@
+2016-04-23 Charles Plessy <plessy@riken.jp>
+ * Increment minor version number to trigger update.
+
2016-04-17 Charles Plessy <plessy@riken.jp>
* Added citation information.
* Point URL to the Branchable homepage.
diff --git a/DESCRIPTION b/DESCRIPTION
index 1d65d56..2f4b79c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.9.0
-Date: 2016-04-17
+Version: 1.9.1
+Date: 2016-04-23
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
Description: High throughput analysis of T cell antigen receptor sequences
</pre>
</div>
change to NEWS on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_41c084d4850a27dc41076905be69fcecdd9f4923/
c.plessy
2016-04-17T14:58:26Z
2016-04-17T14:58:26Z
<div id="change-41c084d4850a27dc41076905be69fcecdd9f4923" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=NEWS;h=d26b239602edde554ec52d1d7b39f0780a0435e3;hp=1f8f4010e77119f41dd414e87642e191b48f83b8;hb=41c084d4850a27dc41076905be69fcecdd9f4923;hpb=828dd73e4732b0fb8cda585994bd18a8008c8f81" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=NEWS" rel="nofollow">NEWS</a>
</span>
<span class="desc"><br />Changed by:</span>
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<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-04-17T14:58:26Z" class="relativedate" title="Sun, 17 Apr 2016 14:58:26 +0000">14:58:26 04/17/16</time></span>
<span class="desc"><br /></span>
<span class="revert">
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</span>
</div>
<div class="changelog">
Updated NEWS page.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@116419 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/NEWS b/NEWS
index 1f8f401..d26b239 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.10.0
+
+OTHER CHANGES
+
+ o Minor metadata updates.
+
Changes in version 1.8.0
NEW FEATURES
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_828dd73e4732b0fb8cda585994bd18a8008c8f81/
c.plessy
2016-04-17T14:57:16Z
2016-04-17T14:57:16Z
<div id="change-828dd73e4732b0fb8cda585994bd18a8008c8f81" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=1d65d568b17247fc862f2c50eb53dce2d2797188;hp=cda02f5fc6992b4b8a3028a9eedffbbd99586df2;hb=828dd73e4732b0fb8cda585994bd18a8008c8f81;hpb=94a3f80ac9787708d669b3f7ae9a37a5508ebb4e" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-04-17T14:57:16Z" class="relativedate" title="Sun, 17 Apr 2016 14:57:16 +0000">14:57:16 04/17/16</time></span>
<span class="desc"><br /></span>
<span class="revert">
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</span>
</div>
<div class="changelog">
Added URL in DESCRIPTION and updated data.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@116418 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index cda02f5..1d65d56 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
Version: 1.9.0
-Date: 2015-10-06
+Date: 2016-04-17
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
Description: High throughput analysis of T cell antigen receptor sequences
@@ -20,4 +20,5 @@ Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
VignetteBuilder: knitr
Packaged: 2013-12-11 10:22:39 UTC; charles
biocViews: Sequencing
+URL: http://clonotyper.branchable.com/
BugReports: http://clonotyper.branchable.com/Bugs/
</pre>
</div>
change to ChangeLog on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_94a3f80ac9787708d669b3f7ae9a37a5508ebb4e/
c.plessy
2016-04-17T14:56:52Z
2016-04-17T14:56:52Z
<div id="change-94a3f80ac9787708d669b3f7ae9a37a5508ebb4e" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=ChangeLog;h=3fad6518bb98ed2b28bb513f4340cf016279b0c1;hp=06e2de00bc53e5b1b5dc473b28d74d031ce16ae1;hb=94a3f80ac9787708d669b3f7ae9a37a5508ebb4e;hpb=a337f3414099576c2dfe5a561fa5240b247d57b5" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=ChangeLog" rel="nofollow">ChangeLog</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=c.plessy" rel="nofollow">c.plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-04-17T14:56:52Z" class="relativedate" title="Sun, 17 Apr 2016 14:56:52 +0000">14:56:52 04/17/16</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Updated changelog.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@116417 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/ChangeLog b/ChangeLog
index 06e2de0..3fad651 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+2016-04-17 Charles Plessy <plessy@riken.jp>
+ * Added citation information.
+ * Point URL to the Branchable homepage.
+
+2015-02-05 Charles Plessy <plessy@riken.jp>
+ * Aded the function private_clonotypes().
+
2014-09-25 Charles Plessy <plessy@riken.jp>
* Version 1.3.2
* Import “methods” instead of depending on.
</pre>
</div>
change to inst/CITATION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_a337f3414099576c2dfe5a561fa5240b247d57b5/
c.plessy
2016-04-17T14:46:54Z
2016-04-17T14:46:54Z
<div id="change-a337f3414099576c2dfe5a561fa5240b247d57b5" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=inst/CITATION;h=52cdbf0f0efed82470c480d13f971793d4e2fc07;hp=0000000000000000000000000000000000000000;hb=a337f3414099576c2dfe5a561fa5240b247d57b5;hpb=483c3cea97d2596a36b20c6a93a7a65a780cd36e" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=inst%2FCITATION" rel="nofollow">inst/CITATION</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-04-17T14:46:54Z" class="relativedate" title="Sun, 17 Apr 2016 14:46:54 +0000">14:46:54 04/17/16</time></span>
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</span>
</div>
<div class="changelog">
Preprint released in biorXiv.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@116416 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000..52cdbf0
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,16 @@
+citEntry( entry = "article"
+ , author = "Plessy, Charles and Mariotti-Ferrandiz, Encarnita and Manabe, Ri-Ichiroh and Hori, Shohei"
+ , title = "clonotypeR--high throughput analysis of T cell antigen receptor sequences"
+ , year = "2015"
+ , doi = "10.1101/028696"
+ , publisher = "Cold Spring Harbor Labs Journals"
+ , abstract = "Motivation The T cell receptors are expressed as millions of different rearrangements. Amplified as a complex mixture of PCR products, they can be sequenced directly on next-generation instruments without the need for cloning. This method is increasingly used to characterize, quantify and study these highly diverse receptors. Results We present here clonotypeR, a software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents a the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc. To analyze clonotype data at the nucleotide level, we introduce unique clonotype identifiers based on those developed by Yassai et al. (2009), that we corrected to avoid identifier collisions. Availability http://clonotyper.branchable.com (CC0 license)."
+ , URL = "http://www.biorxiv.org/content/early/2015/10/08/028696"
+ , eprint = "http://www.biorxiv.org/content/early/2015/10/08/028696.full.pdf"
+ , journal = "bioRxiv"
+ , textVersion = paste( "clonotypeR--high throughput analysis of T cell antigen receptor sequences."
+ , "Charles Plessy, Encarnita Mariotti-Ferrandiz, Ri-Ichiroh Manabe, Shohei Hori."
+ , "bioRxiv doi: http://dx.doi.org/10.1101/028696"
+ , "This article is a preprint and has not been peer-reviewed."
+ )
+ )
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_4c01b3aab3918894565c9df6c03fd6067c971e87/
https://launchpad.net/~plessy
2016-03-31T00:40:28Z
2016-03-31T00:40:28Z
<div id="change-4c01b3aab3918894565c9df6c03fd6067c971e87" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=index.mdwn;h=47453943f790fd4c105bbb1942e5a451740ca5c3;hp=428ac8e705f18ce34d4505f89c04005f0f160108;hb=4c01b3aab3918894565c9df6c03fd6067c971e87;hpb=d602071f796a8b0f7486d4e9e8a51547d31918a1" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=index" rel="nofollow">index</a>
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<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-03-31T00:40:28Z" class="relativedate" title="Thu, 31 Mar 2016 00:40:28 +0000">00:40:28 03/31/16</time></span>
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</span>
</div>
<div class="changelog">
CDJtools<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 428ac8e..4745394 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -38,8 +38,9 @@ to try alternative solutions, you can have a look at
[[IMGTHighV-QUEST|http://www.imgt.org/IMGTindex/IMGTHighV-QUEST.html]],
[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
[MiTCR](http://mitcr.milaboratory.com/),
-[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html), or
-[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full).
+[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
+[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full), or
+[VDJtools](https://github.com/mikessh/vdjtools).
See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
*clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_d602071f796a8b0f7486d4e9e8a51547d31918a1/
https://launchpad.net/~plessy
2016-02-29T08:07:32Z
2016-02-29T08:07:32Z
<div id="change-d602071f796a8b0f7486d4e9e8a51547d31918a1" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2016-02-29T08:07:32Z" class="relativedate" title="Mon, 29 Feb 2016 08:07:32 +0000">08:07:32 02/29/16</time></span>
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<div class="changelog">
List LymAnalyzer, but did not test.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 82bf104..428ac8e 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -37,8 +37,9 @@ RIKEN about shortcomings, limitations, or possible developments. If you need
to try alternative solutions, you can have a look at
[[IMGTHighV-QUEST|http://www.imgt.org/IMGTindex/IMGTHighV-QUEST.html]],
[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
-[MiTCR](http://mitcr.milaboratory.com/), or
-[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html).
+[MiTCR](http://mitcr.milaboratory.com/),
+[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html), or
+[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full).
See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
*clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).
</pre>
</div>
change to references/README on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_147f5c04f31d96cc9240130ed8df67c9f1ae96c3/
https://launchpad.net/~plessy
2015-11-17T01:33:45Z
2015-11-17T01:33:45Z
<div id="change-147f5c04f31d96cc9240130ed8df67c9f1ae96c3" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=references/README.mdwn;h=d357a9d87547f2b6398487bb27614214a80b3d4e;hp=a256479f14bb5e1303a169d158595591358ccdde;hb=147f5c04f31d96cc9240130ed8df67c9f1ae96c3;hpb=72e72f10ee9a617cca51ec6fe600940795421e41" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=references%2FREADME" rel="nofollow">references/README</a>
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<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-11-17T01:33:45Z" class="relativedate" title="Tue, 17 Nov 2015 01:33:45 +0000">01:33:45 11/17/15</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=revert&rev=147f5c04f31d96cc9240130ed8df67c9f1ae96c3" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Use ikiwiki syntax for image display and plain Markdown as fallback just in case.<br />
</div>
<div class="diff">
<pre>
diff --git a/references/README.mdwn b/references/README.mdwn
index a256479..d357a9d 100644
--- a/references/README.mdwn
+++ b/references/README.mdwn
@@ -9,8 +9,10 @@ The references sequences are [TRA@.gb][Mmus_TRA], [TRB@.gb][Mmus_TRB] and
files with full information from the NCBI's website, select _Show sequence_ and
_GenBank (full)_ as shown in the panels below.
-![How to select "Show sequence"](NCBI_Show_sequence.png)
-![How to select "GenBank (full)"](NCBI_Save_GenBank_full.png)
+[[!img NCBI_Show_sequence.png alt='How to select "Show sequence"' link='no']]
+![](NCBI_Show_sequence.png)
+[[!img NCBI_Save_GenBank_full.png alt='How to select "GenBank (full)"' link='no']]
+![](NCBI_Save_GenBank_full.png)
The *V*, *(D)*, *J* and *C* segments were extracted with the command `make
gb2fa`, wich uses the the [extractfeat][] program of the EMBOSS package.
</pre>
</div>
change to references/TRG@.gb on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_05318e4d6a1180a10bfa4ea6d4b4ecff13ab9a7c/
plessy
2015-11-17T01:16:58Z
2015-11-17T01:16:58Z
<div id="change-05318e4d6a1180a10bfa4ea6d4b4ecff13ab9a7c" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=references/TRG%40.gb;h=ff43dad775481e0a8afd9b9d95ec472334586b7b;hp=9d48fafbb7e4209a462dbb1ab552195c00e920e3;hb=05318e4d6a1180a10bfa4ea6d4b4ecff13ab9a7c;hpb=4c57fa302630a06a718076885900e8a719bd9904" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=references%2FTRG%40.gb" rel="nofollow">references/TRG@.gb</a>
</span>
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-11-17T01:16:58Z" class="relativedate" title="Tue, 17 Nov 2015 01:16:58 +0000">01:16:58 11/17/15</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Updated from RefSeq.<br />
No notable changes for clonotpyeR.<br />
</div>
<div class="diff">
<pre>
diff --git a/references/TRG@.gb b/references/TRG@.gb
index 9d48faf..ff43dad 100644
--- a/references/TRG@.gb
+++ b/references/TRG@.gb
@@ -1,4 +1,4 @@
-LOCUS NG_007033 179435 bp DNA linear CON 03-NOV-2013
+LOCUS NG_007033 179435 bp DNA linear CON 29-DEC-2013
DEFINITION Mus musculus T cell receptor gamma chain (Tcrg) on chromosome 13.
ACCESSION NG_007033
VERSION NG_007033.1 GI:159120306
@@ -46,14 +46,15 @@ REFERENCE 4 (bases 1 to 179435)
REMARK GeneRIF: Gamma delta receptor loss in T-cells are involved in hair
cycling defects.
REFERENCE 5 (bases 1 to 179435)
- AUTHORS Jeong,S.P., Kang,J.A. and Park,S.G.
- TITLE Intestinal intraepithelial TCRgammadelta(+) T cells are activated
- by normal commensal bacteria
- JOURNAL J. Microbiol. 50 (5), 837-841 (2012)
- PUBMED 23124753
- REMARK GeneRIF: TCRgammadelta(+) T cell population attached to the
- intestinal lumen is constitutively activated by normal commensal
- bacteria.
+ AUTHORS Laird,R.M., Wolf,B.J., Princiotta,M.F. and Hayes,S.M.
+ TITLE gammadelta T cells acquire effector fates in the thymus and
+ differentiate into cytokine-producing effectors in a Listeria model
+ of infection independently of CD28 costimulation
+ JOURNAL PLoS ONE 8 (5), E63178 (2013)
+ PUBMED 23671671
+ REMARK GeneRIF: Data indicate that CD28 is dispensable for gammadelta
+ effector T cell development and differentiation.
+ Publication Status: Online-Only
REFERENCE 6 (bases 1 to 179435)
AUTHORS Johnson,K.R. and Davisson,M.T.
TITLE A multipoint genetic linkage map of mouse chromosome 18
@@ -114,8 +115,8 @@ COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
publications that are available for this gene. Please see the Gene
record to access additional publications.
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
- 1-61826 AC122849.4 140943-202768
- 61827-179435 AC146604.5 30325-147933
+ 1-61826 AC071805.4 140943-202768
+ 61827-179435 AC131072.5 30325-147933
FEATURES Location/Qualifiers
source 1..179435
/organism="Mus musculus"
@@ -128,14 +129,14 @@ FEATURES Location/Qualifiers
/gene_synonym="TCRGV1S1; TCRGV2S1; TCRGV3S1; TCRGV5S3"
/note="T cell receptor gamma chain"
/db_xref="GeneID:110067"
- /db_xref="MGI:98623"
+ /db_xref="MGI:MGI:98623"
gene 501..951
/gene="Tcrg-V7"
/gene_synonym="TRGV7; Vg7"
/note="T cell receptor gamma, variable 7"
/db_xref="GeneID:21641"
/db_xref="IMGT/GENE-DB:TRGV7"
- /db_xref="MGI:98637"
+ /db_xref="MGI:MGI:98637"
CDS join(501..543,645..951)
/gene="Tcrg-V7"
/gene_synonym="TRGV7; Vg7"
@@ -143,7 +144,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:21641"
/db_xref="IMGT/GENE-DB:TRGV7"
- /db_xref="MGI:98637"
+ /db_xref="MGI:MGI:98637"
V_segment join(501..543,645..951)
/gene="Tcrg-V7"
/gene_synonym="TRGV7; Vg7"
@@ -154,7 +155,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma, variable 4"
/db_xref="GeneID:21638"
/db_xref="IMGT/GENE-DB:TRGV4"
- /db_xref="MGI:98634"
+ /db_xref="MGI:MGI:98634"
CDS join(7440..7551,7659..7965)
/gene="Tcrg-V4"
/gene_synonym="AI528624; TRGV4; Vg4"
@@ -162,7 +163,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:21638"
/db_xref="IMGT/GENE-DB:TRGV4"
- /db_xref="MGI:98634"
+ /db_xref="MGI:MGI:98634"
V_segment join(7440..7551,7659..7965)
/gene="Tcrg-V4"
/gene_synonym="AI528624; TRGV4; Vg4"
@@ -173,7 +174,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma, variable 6"
/db_xref="GeneID:21640"
/db_xref="IMGT/GENE-DB:TRGV6"
- /db_xref="MGI:98636"
+ /db_xref="MGI:MGI:98636"
CDS join(12827..12920,13077..13388)
/gene="Tcrg-V6"
/gene_synonym="TRGV6"
@@ -181,7 +182,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:21640"
/db_xref="IMGT/GENE-DB:TRGV6"
- /db_xref="MGI:98636"
+ /db_xref="MGI:MGI:98636"
V_segment join(12827..12920,13077..13388)
/gene="Tcrg-V6"
/gene_synonym="TRGV6"
@@ -192,7 +193,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma, variable 5"
/db_xref="GeneID:21639"
/db_xref="IMGT/GENE-DB:TRGV5"
- /db_xref="MGI:98635"
+ /db_xref="MGI:MGI:98635"
CDS join(14737..14779,14887..15184)
/gene="Tcrg-V5"
/gene_synonym="TRGV5"
@@ -200,7 +201,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:21639"
/db_xref="IMGT/GENE-DB:TRGV5"
- /db_xref="MGI:98635"
+ /db_xref="MGI:MGI:98635"
V_segment join(14737..14779,14887..15184)
/gene="Tcrg-V5"
/gene_synonym="TRGV5"
@@ -211,7 +212,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma joining 1"
/db_xref="GeneID:100126431"
/db_xref="IMGT/GENE-DB:TRGJ1"
- /db_xref="MGI:4440480"
+ /db_xref="MGI:MGI:4440480"
CDS 32802..32861
/gene="Trgj1"
/gene_synonym="Gm17003"
@@ -219,7 +220,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:100126431"
/db_xref="IMGT/GENE-DB:TRGJ1"
- /db_xref="MGI:4440480"
+ /db_xref="MGI:MGI:4440480"
J_segment 32802..32861
/gene="Trgj1"
/gene_synonym="Gm17003"
@@ -230,7 +231,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma, constant 1"
/db_xref="GeneID:107573"
/db_xref="IMGT/GENE-DB:TRGC1"
- /db_xref="MGI:98625"
+ /db_xref="MGI:MGI:98625"
CDS join(36562..36891,38323..38367,38935..39077)
/gene="Tcrg-C1"
/gene_synonym="Cgamma1; Gm17004; TRGC1"
@@ -238,7 +239,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:107573"
/db_xref="IMGT/GENE-DB:TRGC1"
- /db_xref="MGI:98625"
+ /db_xref="MGI:MGI:98625"
C_region join(36562..36891,38323..38367,38935..39077)
/gene="Tcrg-C1"
/gene_synonym="Cgamma1; Gm17004; TRGC1"
@@ -248,7 +249,8 @@ FEATURES Location/Qualifiers
/gene_synonym="Cgamma1; Gm17004; TRGC1"
/standard_name="PMC156147P8"
/db_xref="UniSTS:271385"
- enhancer 41876..42875
+ regulatory 41876..42875
+ /regulatory_class="enhancer"
/gene="Tcrg"
/gene_synonym="TCRGV1S1; TCRGV2S1; TCRGV3S1; TCRGV5S3"
/note="gamma 1 enhancer"
@@ -258,7 +260,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma, variable 3"
/db_xref="GeneID:21637"
/db_xref="IMGT/GENE-DB:TRGV3"
- /db_xref="MGI:98633"
+ /db_xref="MGI:MGI:98633"
CDS join(65304..65349,65454..65760)
/gene="Tcrg-V3"
/gene_synonym="TCRGV5S3; TRGV3; vgamma3"
@@ -266,7 +268,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:21637"
/db_xref="IMGT/GENE-DB:TRGV3"
- /db_xref="MGI:98633"
+ /db_xref="MGI:MGI:98633"
V_segment join(65304..65349,65454..65760)
/gene="Tcrg-V3"
/gene_synonym="TCRGV5S3; TRGV3; vgamma3"
@@ -277,7 +279,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor gamma joining 3"
/db_xref="GeneID:100126432"
/db_xref="IMGT/GENE-DB:TRGJ3"
- /db_xref="MGI:4439528"
+ /db_xref="MGI:MGI:4439528"
CDS 79576..79635
/gene="Trgj3"
/gene_synonym="Gm16604"
@@ -285,7 +287,7 @@ FEATURES Location/Qualifiers
/codon_start=1
(Diff truncated)
</pre>
</div>
change to references/TRB@.gb on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_4c57fa302630a06a718076885900e8a719bd9904/
plessy
2015-11-17T01:10:11Z
2015-11-17T01:10:11Z
<div id="change-4c57fa302630a06a718076885900e8a719bd9904" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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Updated TRB@ locus from RefSeq.<br />
Notable change: Trbv31 sequence corrected (following ticket 16738599<br />
submitted by me)<br />
</div>
<div class="diff">
<pre>
diff --git a/references/TRB@.gb b/references/TRB@.gb
index 0f9255e..f4d8b3c 100644
--- a/references/TRB@.gb
+++ b/references/TRB@.gb
@@ -1,4 +1,4 @@
-LOCUS NG_006980 668076 bp DNA linear CON 05-NOV-2013
+LOCUS NG_006980 668076 bp DNA linear CON 05-NOV-2015
DEFINITION Mus musculus T cell receptor beta chain (Tcrb) on chromosome 6.
ACCESSION NG_006980
VERSION NG_006980.1 GI:158037406
@@ -9,74 +9,88 @@ SOURCE Mus musculus (house mouse)
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE 1 (bases 1 to 668076)
- AUTHORS Hess,C., Winkler,A., Lorenz,A.K., Holecska,V., Blanchard,V.,
- Eiglmeier,S., Schoen,A.L., Bitterling,J., Stoehr,A.D., Petzold,D.,
- Schommartz,T., Mertes,M.M., Schoen,C.T., Tiburzy,B., Herrmann,A.,
- Kohl,J., Manz,R.A., Madaio,M.P., Berger,M., Wardemann,H. and
- Ehlers,M.
- TITLE T cell-independent B cell activation induces immunosuppressive
- sialylated IgG antibodies
- JOURNAL J. Clin. Invest. 123 (9), 3788-3796 (2013)
- PUBMED 23979161
+ AUTHORS Mallis RJ, Bai K, Arthanari H, Hussey RE, Handley M, Li Z,
+ Chingozha L, Duke-Cohan JS, Lu H, Wang JH, Zhu C, Wagner G and
+ Reinherz EL.
+ TITLE Pre-TCR ligand binding impacts thymocyte development before
+ alphabetaTCR expression
+ JOURNAL Proc. Natl. Acad. Sci. U.S.A. 112 (27), 8373-8378 (2015)
+ PUBMED 26056289
+ REMARK GeneRIF: Data show that the pre-T-cell receptor (preTCR), a
+ pTalpha-beta heterodimer appearing before alphabetaTCR expression,
+ directs initial phase of repertoire selection.
REFERENCE 2 (bases 1 to 668076)
- AUTHORS Hickey,A.J., Lin,J.S., Kummer,L.W., Szaba,F.M., Duso,D.K.,
- Tighe,M., Parent,M.A. and Smiley,S.T.
- TITLE Intranasal prophylaxis with CpG oligodeoxynucleotide can protect
- against Yersinia pestis infection
- JOURNAL Infect. Immun. 81 (6), 2123-2132 (2013)
- PUBMED 23545300
+ AUTHORS Bergot AS, Chaara W, Ruggiero E, Mariotti-Ferrandiz E, Dulauroy S,
+ Schmidt M, von Kalle C, Six A and Klatzmann D.
+ TITLE TCR sequences and tissue distribution discriminate the subsets of
+ naive and activated/memory Treg cells in mice
+ JOURNAL Eur. J. Immunol. 45 (5), 1524-1534 (2015)
+ PUBMED 25726757
+ REMARK GeneRIF: in deep- versus superficial lymph nodes, TCR-beta deep
+ sequencing revealed diversified naive Treg-cell and
+ activated-memory Treg-cell repertoires
REFERENCE 3 (bases 1 to 668076)
- AUTHORS Archer,N.K., Harro,J.M. and Shirtliff,M.E.
- TITLE Clearance of Staphylococcus aureus nasal carriage is T cell
- dependent and mediated through interleukin-17A expression and
- neutrophil influx
- JOURNAL Infect. Immun. 81 (6), 2070-2075 (2013)
- PUBMED 23529621
+ AUTHORS Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG,
+ Montpellier B, Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel
+ MS and Guidos CJ.
+ TITLE IL-7 coordinates proliferation, differentiation and Tcra
+ recombination during thymocyte beta-selection
+ JOURNAL Nat. Immunol. 16 (4), 397-405 (2015)
+ PUBMED 25729925
+ REMARK GeneRIF: IL-7 critically acts cooperatively with signaling via the
+ pre-TCR and Notch1 to coordinate proliferation, differentiation and
+ TCRalpha recombination during beta-selection.
REFERENCE 4 (bases 1 to 668076)
- AUTHORS Larson,R.P., Comeau,M.R. and Ziegler,S.F.
- TITLE Cutting edge: allergen-specific CD4 T cells respond indirectly to
- thymic stromal lymphopoietin to promote allergic responses in the
- skin
- JOURNAL J. Immunol. 190 (9), 4474-4477 (2013)
- PUBMED 23543759
+ AUTHORS Guenova E, Skabytska Y, Hoetzenecker W, Weindl G, Sauer K, Tham M,
+ Kim KW, Park JH, Seo JH, Ignatova D, Cozzio A, Levesque MP, Volz T,
+ Koberle M, Kaesler S, Thomas P, Mailhammer R, Ghoreschi K, Schakel
+ K, Amarov B, Eichner M, Schaller M, Clark RA, Rocken M and
+ Biedermann T.
+ TITLE IL-4 abrogates T(H)17 cell-mediated inflammation by selective
+ silencing of IL-23 in antigen-presenting cells
+ JOURNAL Proc. Natl. Acad. Sci. U.S.A. 112 (7), 2163-2168 (2015)
+ PUBMED 25646481
REFERENCE 5 (bases 1 to 668076)
- AUTHORS Brady,B.L., Rupp,L.J. and Bassing,C.H.
- TITLE Requirement for dicer in survival of proliferating thymocytes
- experiencing DNA double-strand breaks
- JOURNAL J. Immunol. 190 (7), 3256-3266 (2013)
- PUBMED 23427252
+ AUTHORS Khairnar V, Duhan V, Maney SK, Honke N, Shaabani N, Pandyra AA,
+ Seifert M, Pozdeev V, Xu HC, Sharma P, Baldin F, Marquardsen F,
+ Merches K, Lang E, Kirschning C, Westendorf AM, Haussinger D, Lang
+ F, Dittmer U, Kuppers R, Recher M, Hardt C, Scheffrahn I,
+ Beauchemin N, Gothert JR, Singer BB, Lang PA and Lang KS.
+ TITLE CEACAM1 induces B-cell survival and is essential for protective
+ antiviral antibody production
+ JOURNAL Nat Commun 6, 6217 (2015)
+ PUBMED 25692415
+ REMARK Publication Status: Online-Only
REFERENCE 6 (bases 1 to 668076)
- AUTHORS Acha-Orbea,H., Scarpellino,L., Shakhov,A.N., Held,W. and
- MacDonald,H.R.
+ AUTHORS Acha-Orbea H, Scarpellino L, Shakhov AN, Held W and MacDonald HR.
TITLE Inhibition of mouse mammary tumor virus-induced T cell responses in
vivo by antibodies to an open reading frame protein
JOURNAL J. Exp. Med. 176 (6), 1769-1772 (1992)
PUBMED 1334118
REFERENCE 7 (bases 1 to 668076)
- AUTHORS Mombaerts,P., Clarke,A.R., Rudnicki,M.A., Iacomini,J., Itohara,S.,
- Lafaille,J.J., Wang,L., Ichikawa,Y., Jaenisch,R., Hooper,M.L. et
- al.
+ AUTHORS Mombaerts P, Clarke AR, Rudnicki MA, Iacomini J, Itohara S,
+ Lafaille JJ, Wang L, Ichikawa Y, Jaenisch R, Hooper ML et al.
TITLE Mutations in T-cell antigen receptor genes alpha and beta block
thymocyte development at different stages
JOURNAL Nature 360 (6401), 225-231 (1992)
PUBMED 1359428
REMARK Erratum:[Nature 1992 Dec 3;360(6403):491]
REFERENCE 8 (bases 1 to 668076)
- AUTHORS Ossendorp,F., Jacobs,H., van der Horst,G., de Vries,E., Berns,A.
- and Borst,J.
+ AUTHORS Ossendorp F, Jacobs H, van der Horst G, de Vries E, Berns A and
+ Borst J.
TITLE T cell receptor-alpha beta lacking the beta-chain V domain can be
expressed at the cell surface but prohibits T cell maturation
JOURNAL J. Immunol. 148 (12), 3714-3722 (1992)
PUBMED 1351085
REFERENCE 9 (bases 1 to 668076)
- AUTHORS Suzuki,M., Koseki,H., Mizutani,Y., Kuribayashi,K., Kanno,M. and
- Taniguchi,M.
+ AUTHORS Suzuki M, Koseki H, Mizutani Y, Kuribayashi K, Kanno M and
+ Taniguchi M.
TITLE Expansion of murine T cells bearing a unique T cell receptor
beta-chain in Friend virus-induced tumor in situ
JOURNAL J. Immunol. 148 (9), 2968-2973 (1992)
PUBMED 1374106
REFERENCE 10 (bases 1 to 668076)
- AUTHORS Waters,S.H., O'Neil,J.J., Melican,D.T. and Appel,M.C.
+ AUTHORS Waters SH, O'Neil JJ, Melican DT and Appel MC.
TITLE Multiple TCR V beta usage by infiltrates of young NOD mouse islets
of Langerhans. A polymerase chain reaction analysis
JOURNAL Diabetes 41 (3), 308-312 (1992)
@@ -114,13 +128,13 @@ COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
publications that are available for this gene. Please see the Gene
record to access additional publications.
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
- 1-40285 AC161887.5 187467-227751
- 40286-148984 AC161768.25 87370-196068
- 148985-267619 AC153851.27 99220-217854
- 267620-433004 AC125228.4 96216-261600
- 433005-559515 AC158659.6 1-126511 c
- 559516-635734 AC153854.7 105046-181264
- 635735-668076 AC117678.16 48698-81039
+ 1-40285 AC157861.5 187467-227751
+ 40286-148984 AC131072.25 87370-196068
+ 148985-267619 AC131072.27 99220-217854
+ 267620-433004 AC065536.4 96216-261600
+ 433005-559515 AC131072.6 1-126511 c
+ 559516-635734 AC131072.7 105046-181264
+ 635735-668076 AC065536.16 48698-81039
FEATURES Location/Qualifiers
source 1..668076
/organism="Mus musculus"
@@ -133,14 +147,14 @@ FEATURES Location/Qualifiers
/gene_synonym="TCRbeta; Tib"
/note="T cell receptor beta chain"
/db_xref="GeneID:21577"
- /db_xref="MGI:98578"
+ /db_xref="MGI:MGI:98578"
gene 502..1091
/gene="Trbv1"
/gene_synonym="621968; Gm6273; Tcrb-V2; TCRBV2S1"
/note="T cell receptor beta, variable 1"
/db_xref="GeneID:621968"
/db_xref="IMGT/GENE-DB:TRBV1"
- /db_xref="MGI:98594"
+ /db_xref="MGI:MGI:98594"
CDS join(502..556,797..1091)
/gene="Trbv1"
/gene_synonym="621968; Gm6273; Tcrb-V2; TCRBV2S1"
@@ -148,7 +162,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:621968"
/db_xref="IMGT/GENE-DB:TRBV1"
- /db_xref="MGI:98594"
+ /db_xref="MGI:MGI:98594"
V_segment join(502..556,797..1091)
/gene="Trbv1"
/gene_synonym="621968; Gm6273; Tcrb-V2; TCRBV2S1"
@@ -158,7 +172,7 @@ FEATURES Location/Qualifiers
/gene_synonym="1700020H15; Tryx3"
/note="protease, serine 58"
/db_xref="GeneID:232717"
- /db_xref="MGI:3608323"
+ /db_xref="MGI:MGI:3608323"
mRNA complement(join(4468..4717,4801..4940,6511..6767,
6933..7071,9260..9344,9478..9593))
/gene="Prss58"
@@ -167,7 +181,7 @@ FEATURES Location/Qualifiers
/transcript_id="NM_175020.3"
/db_xref="GI:146198660"
(Diff truncated)
</pre>
</div>
change to references/NCBI_Save_GenBank_full.png references/NCBI_Show_sequence.png references/README on clonotypeR
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plessy
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Screen capture showing how to export the GenBank files.<br />
</div>
<div class="diff">
<pre>
diff --git a/references/NCBI_Save_GenBank_full.png b/references/NCBI_Save_GenBank_full.png
new file mode 100644
index 0000000..9f7a6bd
Binary files /dev/null and b/references/NCBI_Save_GenBank_full.png differ
diff --git a/references/NCBI_Show_sequence.png b/references/NCBI_Show_sequence.png
new file mode 100644
index 0000000..22815c4
Binary files /dev/null and b/references/NCBI_Show_sequence.png differ
diff --git a/references/README.mdwn b/references/README.mdwn
index 8f7211a..a256479 100644
--- a/references/README.mdwn
+++ b/references/README.mdwn
@@ -5,9 +5,15 @@ Mus musculus
------------
The references sequences are [TRA@.gb][Mmus_TRA], [TRB@.gb][Mmus_TRB] and
-[TRG@.gb][Mmus_TRG], downloaded in GenBank format from [RefSeq][]. The *V*, *(D)*, *J* and *C* segments were
-extracted with the command `make gb2fa`, wich uses the the [extractfeat][]
-program of the EMBOSS package.
+[TRG@.gb][Mmus_TRG], downloaded in GenBank format from [RefSeq][]. To save the
+files with full information from the NCBI's website, select _Show sequence_ and
+_GenBank (full)_ as shown in the panels below.
+
+![How to select "Show sequence"](NCBI_Show_sequence.png)
+![How to select "GenBank (full)"](NCBI_Save_GenBank_full.png)
+
+The *V*, *(D)*, *J* and *C* segments were extracted with the command `make
+gb2fa`, wich uses the the [extractfeat][] program of the EMBOSS package.
This directory contains *V* and *J* segments aligned on conserved motifs in the
files [[V.fa]] and [[J.fa]]. These alignments were made by hand using [[SeaView|doc/seaview]] and
</pre>
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Updated mouse TRA@ record.<br />
Notable change: "Trav21/dv12" is renamed "Trav21-dv12".<br />
</div>
<div class="diff">
<pre>
diff --git a/references/TRA@.gb b/references/TRA@.gb
index f0e1f64..b51e0b6 100644
--- a/references/TRA@.gb
+++ b/references/TRA@.gb
@@ -1,4 +1,4 @@
-LOCUS NG_007044 1797232 bp DNA linear CON 08-JUL-2013
+LOCUS NG_007044 1797232 bp DNA linear CON 30-SEP-2015
DEFINITION Mus musculus T cell receptor alpha delta locus (Tcra/tcrd@) on
chromosome 14.
ACCESSION NG_007044
@@ -10,7 +10,7 @@ SOURCE Mus musculus (house mouse)
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE 1 (bases 1 to 1797232)
- AUTHORS Takeshita,S., Toda,M. and Yamagishi,H.
+ AUTHORS Takeshita S, Toda M and Yamagishi H.
TITLE Excision products of the T cell receptor gene support a progressive
rearrangement model of the alpha/delta locus
JOURNAL EMBO J. 8 (11), 3261-3270 (1989)
@@ -97,14 +97,14 @@ FEATURES Location/Qualifiers
/gene_synonym="Tcralpha"
/note="T cell receptor alpha chain"
/db_xref="GeneID:21473"
- /db_xref="MGI:98553"
+ /db_xref="MGI:MGI:98553"
gene 501..1410
/gene="Trav1"
/gene_synonym="Gm13987; OTTMUSG00000015242"
/note="T cell receptor alpha variable 1"
/db_xref="GeneID:627171"
/db_xref="IMGT/GENE-DB:TRAV1"
- /db_xref="MGI:3651476"
+ /db_xref="MGI:MGI:3651476"
CDS join(501..549,1128..1410)
/gene="Trav1"
/gene_synonym="Gm13987; OTTMUSG00000015242"
@@ -112,7 +112,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:627171"
/db_xref="IMGT/GENE-DB:TRAV1"
- /db_xref="MGI:3651476"
+ /db_xref="MGI:MGI:3651476"
V_segment join(501..549,1128..1410)
/gene="Trav1"
/gene_synonym="Gm13987; OTTMUSG00000015242"
@@ -122,7 +122,7 @@ FEATURES Location/Qualifiers
/gene_synonym="MOR244-3; Mor83; Or83"
/note="olfactory receptor 1509"
/db_xref="GeneID:57271"
- /db_xref="MGI:3031343"
+ /db_xref="MGI:MGI:3031343"
mRNA 22927..23936
/gene="Olfr1509"
/gene_synonym="MOR244-3; Mor83; Or83"
@@ -130,7 +130,7 @@ FEATURES Location/Qualifiers
/transcript_id="NM_020514.2"
/db_xref="GI:282394046"
/db_xref="GeneID:57271"
- /db_xref="MGI:3031343"
+ /db_xref="MGI:MGI:3031343"
STS 22927..23936
/gene="Olfr1509"
/gene_synonym="MOR244-3; Mor83; Or83"
@@ -146,7 +146,7 @@ FEATURES Location/Qualifiers
/db_xref="GI:282394047"
/db_xref="CCDS:CCDS27060.1"
/db_xref="GeneID:57271"
- /db_xref="MGI:3031343"
+ /db_xref="MGI:MGI:3031343"
/translation="MGALNQTRVTEFIFLGLTDNWVLEILFFVPFTVTYMLTLLGNFL
IVVTIVFTPRLHNPMYFFLSNLSFIDICHSSVTVPKMLEGLLLERKTISFDNCIAQLF
FLHLFACSEIFLLTIMAYDRYVAICIPLHYSNVMNMKVCVQLVFALWLGGTIHSLVQT
@@ -163,7 +163,7 @@ FEATURES Location/Qualifiers
/gene_synonym="Mor10; MOR244-2; MOR244-4; Or10"
/note="olfactory receptor 1508"
/db_xref="GeneID:57270"
- /db_xref="MGI:3031342"
+ /db_xref="MGI:MGI:3031342"
mRNA complement(join(35255..36556,39430..39995))
/gene="Olfr1508"
/gene_synonym="Mor10; MOR244-2; MOR244-4; Or10"
@@ -172,7 +172,7 @@ FEATURES Location/Qualifiers
/transcript_id="NM_020513.2"
/db_xref="GI:112821657"
/db_xref="GeneID:57270"
- /db_xref="MGI:3031342"
+ /db_xref="MGI:MGI:3031342"
STS 35562..36634
/gene="Tcra"
/gene_synonym="Tcralpha"
@@ -188,7 +188,7 @@ FEATURES Location/Qualifiers
/db_xref="GI:10048450"
/db_xref="CCDS:CCDS27061.1"
/db_xref="GeneID:57270"
- /db_xref="MGI:3031342"
+ /db_xref="MGI:MGI:3031342"
/translation="MEKAVLINETSVMSFRLTGLSTNPLVQMAVFFIFLIFYVLTLVG
NILIVITIIYDRRLHTPMYFFLSNLSFIDVCHSTVTVPKMLSDTFSEEKLISFDACVV
QMFFLHLFACTEIFLLTVMAYDRYVAICKPLQYMTIMNWKVCMMLAAALWTGGTIHSI
@@ -204,7 +204,7 @@ FEATURES Location/Qualifiers
/gene_synonym="MOR244-1; Mor28; Or28"
/note="olfactory receptor 1507"
/db_xref="GeneID:57269"
- /db_xref="MGI:3031341"
+ /db_xref="MGI:MGI:3031341"
mRNA complement(join(62469..63506,67663..68229))
/gene="Olfr1507"
/gene_synonym="MOR244-1; Mor28; Or28"
@@ -212,7 +212,7 @@ FEATURES Location/Qualifiers
/transcript_id="NM_001170918.1"
/db_xref="GI:283135127"
/db_xref="GeneID:57269"
- /db_xref="MGI:3031341"
+ /db_xref="MGI:MGI:3031341"
mRNA complement(62469..63580)
/gene="Olfr1507"
/gene_synonym="MOR244-1; Mor28; Or28"
@@ -220,7 +220,7 @@ FEATURES Location/Qualifiers
/transcript_id="NM_020512.2"
/db_xref="GI:283135125"
/db_xref="GeneID:57269"
- /db_xref="MGI:3031341"
+ /db_xref="MGI:MGI:3031341"
STS 62469..63580
/gene="Tcra"
/gene_synonym="Tcralpha"
@@ -236,7 +236,7 @@ FEATURES Location/Qualifiers
/db_xref="GI:283135126"
/db_xref="CCDS:CCDS27062.1"
/db_xref="GeneID:57269"
- /db_xref="MGI:3031341"
+ /db_xref="MGI:MGI:3031341"
/translation="MEKAVLINQTSVMSFRLTGLSTNPKVQMAIFFIFLIFYVLTLVG
NILIVITIIHDHRLHTPMYFFLSNLSFIDVCHSTVTVPKMLSDTFSEEKLISFDDCVV
QIFFLHLFACTEIFLLTVMAYDRYVAICKPLRYMTIMNWKVCMVLGGAMWTAGTIHSI
@@ -254,7 +254,7 @@ FEATURES Location/Qualifiers
/db_xref="GI:283135128"
/db_xref="CCDS:CCDS27062.1"
/db_xref="GeneID:57269"
- /db_xref="MGI:3031341"
+ /db_xref="MGI:MGI:3031341"
/translation="MEKAVLINQTSVMSFRLTGLSTNPKVQMAIFFIFLIFYVLTLVG
NILIVITIIHDHRLHTPMYFFLSNLSFIDVCHSTVTVPKMLSDTFSEEKLISFDDCVV
QIFFLHLFACTEIFLLTVMAYDRYVAICKPLRYMTIMNWKVCMVLGGAMWTAGTIHSI
@@ -272,14 +272,14 @@ FEATURES Location/Qualifiers
/note="predicted gene 9537"
/pseudo
/db_xref="GeneID:671621"
- /db_xref="MGI:3779947"
+ /db_xref="MGI:MGI:3779947"
gene 111186..113410
/gene="Gm7122"
/gene_synonym="EG633692"
/note="predicted pseudogene 7122"
/pseudo
/db_xref="GeneID:633692"
- /db_xref="MGI:3644290"
+ /db_xref="MGI:MGI:3644290"
gene 139827..140587
/gene="Trav2"
/gene_synonym="ENSMUSG00000072561; ENSMUSG00000076759;
@@ -287,7 +287,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor alpha variable 2"
/db_xref="GeneID:100042372"
/db_xref="IMGT/GENE-DB:TRAV2"
- /db_xref="MGI:3642679"
+ /db_xref="MGI:MGI:3642679"
CDS join(139827..139866,140298..140587)
/gene="Trav2"
/gene_synonym="ENSMUSG00000072561; ENSMUSG00000076759;
@@ -296,7 +296,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:100042372"
/db_xref="IMGT/GENE-DB:TRAV2"
- /db_xref="MGI:3642679"
+ /db_xref="MGI:MGI:3642679"
V_segment join(139827..139866,140298..140587)
/gene="Trav2"
/gene_synonym="ENSMUSG00000072561; ENSMUSG00000076759;
@@ -308,7 +308,7 @@ FEATURES Location/Qualifiers
/note="T cell receptor alpha variable 3-1"
/db_xref="GeneID:667441"
/db_xref="IMGT/GENE-DB:TRAV3-1"
- /db_xref="MGI:3644489"
+ /db_xref="MGI:MGI:3644489"
CDS join(153296..153421,153457..153747)
/gene="Trav3-1"
/gene_synonym="EG667441; Gm8635"
@@ -316,7 +316,7 @@ FEATURES Location/Qualifiers
/codon_start=1
/db_xref="GeneID:667441"
/db_xref="IMGT/GENE-DB:TRAV3-1"
- /db_xref="MGI:3644489"
+ /db_xref="MGI:MGI:3644489"
V_segment join(153296..153421,153457..153747)
/gene="Trav3-1"
/gene_synonym="EG667441; Gm8635"
@@ -328,7 +328,7 @@ FEATURES Location/Qualifiers
/pseudo
/db_xref="GeneID:100042384"
(Diff truncated)
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_483c3cea97d2596a36b20c6a93a7a65a780cd36e/
d.tenenbaum
2015-10-13T19:59:53Z
2015-10-13T19:59:53Z
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</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 83ba17e..cda02f5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.8.0
+Version: 1.9.0
Date: 2015-10-06
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_2fd0a315e8908218aa2fb42686a71f3ba6967560/
d.tenenbaum
2015-10-13T19:36:05Z
2015-10-13T19:36:05Z
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</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index b3405df..83ba17e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.7.1
+Version: 1.8.0
Date: 2015-10-06
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to doc/workflow on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_3ca233fb067678b4bd80ae263b0938bdf3a19ea8/
https://launchpad.net/~plessy
2015-10-09T00:25:42Z
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bioRxiv<br />
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<div class="diff">
<pre>
diff --git a/doc/workflow.mdwn b/doc/workflow.mdwn
index c8a42b0..90bea49 100644
--- a/doc/workflow.mdwn
+++ b/doc/workflow.mdwn
@@ -1,7 +1,7 @@
clonotypeR's workflow
=====================
-This workflow summarises the different commands to run. Step-by-step examples using [[test data|doc/examples/with_test_data]] or the [[examples/GSE35626]] public dataset are also available for a more detailed explanation.
+This workflow summarises the different commands to run. Step-by-step examples using [[test data|doc/examples/with_test_data]] or the [[examples/GSE35626]] public dataset are also available for a more detailed explanation. See also the preprint of our [application note deposited in bioRxiv](http://biorxiv.org/content/early/2015/10/08/028696).
Data preparation in the command line
------------------------------------
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_e2c07b19c39f3d8b701d9902bca163807350e9b7/
https://launchpad.net/~plessy
2015-10-09T00:24:42Z
2015-10-09T00:24:42Z
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</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 92fe6a2..82bf104 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -47,6 +47,7 @@ See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a
### Recent news
+ * October 2015: Application note preprint deposited in [bioRxiv](http://biorxiv.org/content/early/2015/10/08/028696).
* October 2014: New stable version [1.4](http://www.bioconductor.org/packages/3.0/bioc/html/clonotypeR.html)
released on Bioconductor.
* 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.
</pre>
</div>
change to .Rbuildignore .gitignore DESCRIPTION NEWS R/private_clonotypes.R man/private_clonotypes.Rd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_bfa79754b0dc52cecbd2cfb8ecbea9f68b3e31cb/
c.plessy
2015-10-06T08:36:41Z
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Commit made by the Bioconductor Git-SVN bridge.<br />
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Increment date and version number.<br />
Commit id: 1f47faad987a4749d15e492a56aac53314ebde83<br />
News for next stable release.<br />
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Roxygen documentation.<br />
Commit id: 8f337a5052bba588e27af72164be92596f547c84<br />
Rstudio...<br />
Commit id: 9b493ce40a9372ecde96e8ab694e52c60d701142<br />
Show where to report bugs.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@109224 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/.Rbuildignore b/.Rbuildignore
index 36312b8..13929dd 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@
Makefile
^references$
^scripts$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index edd4856..fcd14f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
.ikiwiki
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
index dbe503a..b3405df 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.7.0
-Date: 2014-09-25
+Version: 1.7.1
+Date: 2015-10-06
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
Description: High throughput analysis of T cell antigen receptor sequences
@@ -20,3 +20,4 @@ Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
VignetteBuilder: knitr
Packaged: 2013-12-11 10:22:39 UTC; charles
biocViews: Sequencing
+BugReports: http://clonotyper.branchable.com/Bugs/
diff --git a/NEWS b/NEWS
index 4b9b4a2..1f8f401 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.8.0
+
+NEW FEATURES
+
+ o Added a “private_clonotypes” function.
+
Changes in version 1.4.0
BUG FIXES
diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
index 48e28d8..e8eec4e 100644
--- a/R/private_clonotypes.R
+++ b/R/private_clonotypes.R
@@ -1,3 +1,19 @@
+#' private_clonotypes
+#'
+#' List clonotypes found exclusively in one library.
+#'
+#' @param ... Library names.
+#' @param data A clonotype table.
+#'
+#' @return A vector of clonotype names.
+#'
+#' @seealso \code{\link{clonotype_table}}
+#'
+#' @examples
+#' clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+#' clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+#' private_clonotypes("C", data=clonotypes)
+
private_clonotypes <- function (..., data) {
libs <- c(...)
@@ -8,7 +24,7 @@ if ( ! is.character(libs) ) stop (
)
if ( ! is.data.frame(data) ) stop (
- "Second argument must be a data frame of clonotypes."
+ "Data argument must be a data frame of clonotypes."
)
if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
diff --git a/man/private_clonotypes.Rd b/man/private_clonotypes.Rd
new file mode 100644
index 0000000..9fdd23b
--- /dev/null
+++ b/man/private_clonotypes.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/private_clonotypes.R
+\name{private_clonotypes}
+\alias{private_clonotypes}
+\title{private_clonotypes}
+\usage{
+private_clonotypes(..., data)
+}
+\arguments{
+\item{...}{Library names.}
+
+\item{data}{A clonotype table.}
+}
+\value{
+A vector of clonotype names.
+}
+\description{
+List clonotypes found exclusively in one library.
+}
+\examples{
+clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+private_clonotypes("C", data=clonotypes)
+}
+\seealso{
+\code{\link{clonotype_table}}
+}
+
</pre>
</div>
change to DESCRIPTION on clonotypeR
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plessy
2015-10-06T08:34:37Z
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<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 4e3e018..b3405df 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.7.0
-Date: 2014-09-25
+Version: 1.7.1
+Date: 2015-10-06
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
Description: High throughput analysis of T cell antigen receptor sequences
</pre>
</div>
change to NEWS on clonotypeR
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2015-10-06T08:34:03Z
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<div class="diff">
<pre>
diff --git a/NEWS b/NEWS
index 4b9b4a2..1f8f401 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.8.0
+
+NEW FEATURES
+
+ o Added a “private_clonotypes” function.
+
Changes in version 1.4.0
BUG FIXES
</pre>
</div>
change to R/private_clonotypes.R man/private_clonotypes.Rd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_ee840ec5011bd28ffd52e6a3732548008bb89077/
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<div class="diff">
<pre>
diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
index 48e28d8..e8eec4e 100644
--- a/R/private_clonotypes.R
+++ b/R/private_clonotypes.R
@@ -1,3 +1,19 @@
+#' private_clonotypes
+#'
+#' List clonotypes found exclusively in one library.
+#'
+#' @param ... Library names.
+#' @param data A clonotype table.
+#'
+#' @return A vector of clonotype names.
+#'
+#' @seealso \code{\link{clonotype_table}}
+#'
+#' @examples
+#' clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+#' clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+#' private_clonotypes("C", data=clonotypes)
+
private_clonotypes <- function (..., data) {
libs <- c(...)
@@ -8,7 +24,7 @@ if ( ! is.character(libs) ) stop (
)
if ( ! is.data.frame(data) ) stop (
- "Second argument must be a data frame of clonotypes."
+ "Data argument must be a data frame of clonotypes."
)
if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
diff --git a/man/private_clonotypes.Rd b/man/private_clonotypes.Rd
new file mode 100644
index 0000000..9fdd23b
--- /dev/null
+++ b/man/private_clonotypes.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/private_clonotypes.R
+\name{private_clonotypes}
+\alias{private_clonotypes}
+\title{private_clonotypes}
+\usage{
+private_clonotypes(..., data)
+}
+\arguments{
+\item{...}{Library names.}
+
+\item{data}{A clonotype table.}
+}
+\value{
+A vector of clonotype names.
+}
+\description{
+List clonotypes found exclusively in one library.
+}
+\examples{
+clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+private_clonotypes("C", data=clonotypes)
+}
+\seealso{
+\code{\link{clonotype_table}}
+}
+
</pre>
</div>
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2015-10-06T08:27:53Z
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diff --git a/.Rbuildignore b/.Rbuildignore
index 36312b8..13929dd 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@
Makefile
^references$
^scripts$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index edd4856..fcd14f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
.ikiwiki
+.Rproj.user
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diff --git a/DESCRIPTION b/DESCRIPTION
index dbe503a..4e3e018 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,3 +20,4 @@ Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
VignetteBuilder: knitr
Packaged: 2013-12-11 10:22:39 UTC; charles
biocViews: Sequencing
+BugReports: http://clonotyper.branchable.com/Bugs/
</pre>
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diff --git a/index.mdwn b/index.mdwn
index e70b676..92fe6a2 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -8,7 +8,7 @@ in the order of millions, typically produced by Roche 454 instruments, and to
prepare these sequences for differential expression analysis with the typical
transcriptomics tools as well as for statistical analysis using existing [R][] packages.
-[Bioconductor]: http://www.bioconductor.org/packages/release/bioc/html/clonotypeR.html
+[Bioconductor]: https://www.bioconductor.org/packages/clonotypeR
[R]: http://www.r-project.org/ "The R Project for Statistical Computing"
*clonotypeR* is developed in the [RIKEN Yokohama Campus][RIKEN-Yokohama] by the
</pre>
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=index.mdwn;h=e70b6766bc38c1b51f7125bada456baeccf7ff66;hp=5abd66fcba9d294196c2d8ed660985c22c331f25;hb=87cc7c568b2c86ad42ed5f6afc03b309f0423402;hpb=64ac8092a8a0fde9e3f83df3f4a3629081e5922a" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=index" rel="nofollow">index</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-06-27T09:31:39Z" class="relativedate" title="Sat, 27 Jun 2015 09:31:39 +0000">09:31:39 06/27/15</time></span>
<span class="desc"><br /></span>
<span class="revert">
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</span>
</div>
<div class="changelog">
Ling to the omictools website.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 5abd66f..e70b676 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -39,6 +39,7 @@ to try alternative solutions, you can have a look at
[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
[MiTCR](http://mitcr.milaboratory.com/), or
[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html).
+See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
*clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_64ac8092a8a0fde9e3f83df3f4a3629081e5922a/
https://launchpad.net/~plessy
2015-04-24T08:57:48Z
2015-04-24T08:57:48Z
<div id="change-64ac8092a8a0fde9e3f83df3f4a3629081e5922a" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=index.mdwn;h=5abd66fcba9d294196c2d8ed660985c22c331f25;hp=7099cc2ed53d6843c502d629f28b4e99e6f52e33;hb=64ac8092a8a0fde9e3f83df3f4a3629081e5922a;hpb=0c9d84e9f73af79ace54723d9dda56f3e2c2ffd6" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=index&do=goto" rel="nofollow">index</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-04-24T08:57:48Z" class="relativedate" title="Fri, 24 Apr 2015 08:57:48 +0000">08:57:48 04/24/15</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Link to MIGEC.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 7099cc2..5abd66f 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -36,8 +36,9 @@ Plessy|http://genome.gsc.riken.jp/osc/english/members/Charles_Plessy.html]] at
RIKEN about shortcomings, limitations, or possible developments. If you need
to try alternative solutions, you can have a look at
[[IMGTHighV-QUEST|http://www.imgt.org/IMGTindex/IMGTHighV-QUEST.html]],
-[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"), or
-[MiTCR](http://mitcr.milaboratory.com/).
+[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
+[MiTCR](http://mitcr.milaboratory.com/), or
+[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html).
*clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5b5fd86f8ac8cb660cf545fb3dd3364fce71c4d0/
bioc-sync
2015-04-17T04:36:17Z
2015-04-17T04:36:17Z
<div id="change-5b5fd86f8ac8cb660cf545fb3dd3364fce71c4d0" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<span class="desc"><br />Date:</span>
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 0 commit.<br />
Commit information:<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index f304114..dbe503a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.5.0
+Version: 1.7.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_b3cfc4df9df08d97345c23658dba36823a18866f/
d.tenenbaum
2015-04-16T20:02:44Z
2015-04-16T20:02:44Z
<div id="change-b3cfc4df9df08d97345c23658dba36823a18866f" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=dbe503aa9e511be8455500b7befc2c6845c4b45a;hp=2f1eddbf1c3169dea379f70fe32d4d9a2a192c12;hb=b3cfc4df9df08d97345c23658dba36823a18866f;hpb=99f3020ab99f05421229e4f349264c2f23236b90" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
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</span>
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<div class="changelog">
Bump versions in trunk after creation of 3.1 branch.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@102594 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 2f1eddb..dbe503a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.6.0
+Version: 1.7.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_99f3020ab99f05421229e4f349264c2f23236b90/
d.tenenbaum
2015-04-16T19:42:01Z
2015-04-16T19:42:01Z
<div id="change-99f3020ab99f05421229e4f349264c2f23236b90" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=2f1eddbf1c3169dea379f70fe32d4d9a2a192c12;hp=f3041144819bca5c29319076571d814f9ccec6fa;hb=99f3020ab99f05421229e4f349264c2f23236b90;hpb=592f80d92fdc8162818bbf97d794038c1c90a31c" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
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<span class="desc"><br />Changed by:</span>
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</span>
</div>
<div class="changelog">
Bump versions prior to creating 3.1 branch.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@102591 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index f304114..2f1eddb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.5.0
+Version: 1.6.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons. on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_0c9d84e9f73af79ace54723d9dda56f3e2c2ffd6/
http://population-transcriptomics.org/People/Charles_Plessy/
2015-03-19T04:13:01Z
2015-03-19T04:13:01Z
<div id="change-0c9d84e9f73af79ace54723d9dda56f3e2c2ffd6" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn;h=b0afa073b82b605a73beaf1781573f5df06c2f9c;hp=0000000000000000000000000000000000000000;hb=0c9d84e9f73af79ace54723d9dda56f3e2c2ffd6;hpb=121e40090f06ffefdc207f9e7adf94ce5182019b" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FYassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons.&do=goto" rel="nofollow">Bugs/Yassai ID should have no codon ID in absence of non-templated codons.</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-03-19T04:13:01Z" class="relativedate" title="Thu, 19 Mar 2015 04:13:01 +0000">04:13:01 03/19/15</time></span>
<span class="desc"><br /></span>
<span class="revert">
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</span>
</div>
<div class="changelog">
Hmmmm…<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn b/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn
new file mode 100644
index 0000000..b0afa07
--- /dev/null
+++ b/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn
@@ -0,0 +1,6 @@
+<pre>
+> yassai_identifier(c(V="TRAV14N-1", J="TRAJ56", dna="GCAGCTACTGGAGGCAATAATAAGCTGACT", pep="AATGGNNKLT"))
+[1] "aa.1A14N1A56L10"
+</pre>
+
+Should be `aa.A14N1A56L10`.
</pre>
</div>
change to TODO on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_121e40090f06ffefdc207f9e7adf94ce5182019b/
http://population-transcriptomics.org/People/Charles_Plessy/
2015-02-23T06:54:59Z
2015-02-23T06:54:59Z
<div id="change-121e40090f06ffefdc207f9e7adf94ce5182019b" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=TODO.mdwn;h=82495ae02cd85fa5de1361e8183e08002cadfe2e;hp=525db489cb04193c447678bbe8683ce007a9f7a1;hb=121e40090f06ffefdc207f9e7adf94ce5182019b;hpb=9211114ac32036c266d542b9d4b2c6b8c7415215" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=TODO&do=goto" rel="nofollow">TODO</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-02-23T06:54:59Z" class="relativedate" title="Mon, 23 Feb 2015 06:54:59 +0000">06:54:59 02/23/15</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
To do: clonotype algebra ?<br />
</div>
<div class="diff">
<pre>
diff --git a/TODO.mdwn b/TODO.mdwn
index 525db48..82495ae 100644
--- a/TODO.mdwn
+++ b/TODO.mdwn
@@ -44,3 +44,11 @@ compare the number of lines to what is expected.
Support extraction of barcoded reads.
Report the number of V segments found after `clonotypeR detect`.
+
+Clonotype algebra, like in:
+
+<pre>
+`+.clonotypeList` <- function(X, Y) structure( union(X, Y), class='clonotypeList')
+`^.clonotypeList` <- function(X, Y) structure( intersect(X, Y), class='clonotypeList')
+`-.clonotypeList` <- function(X, Y) structure( setdiff(X, Y), class='clonotypeList')
+</pre>
</pre>
</div>
change to R/private_clonotypes.R man/unique_clonotypes.Rd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_592f80d92fdc8162818bbf97d794038c1c90a31c/
c.plessy
2015-02-05T09:56:53Z
2015-02-05T09:56:53Z
<div id="change-592f80d92fdc8162818bbf97d794038c1c90a31c" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=man/unique_clonotypes.Rd;h=2a4d8655aad84f5cabb4cdf839a8bd3ee4dbe7f6;hp=7e5fff937b3351c9efd9f752f3664c0d136949d9;hb=592f80d92fdc8162818bbf97d794038c1c90a31c;hpb=5e276f8999ba8c83cfa09b4f0a58bd2c1e047a47" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=man%2Funique_clonotypes.Rd" rel="nofollow">man/unique clonotypes.Rd</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=c.plessy" rel="nofollow">c.plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-02-05T09:56:53Z" class="relativedate" title="Thu, 05 Feb 2015 09:56:53 +0000">09:56:53 02/05/15</time></span>
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 2 commits.<br />
Commit information:<br />
Commit id: 68cdc95e69dd63e8c1d1698036dd7616a982af38<br />
private_clonotpes: a function to list clonotypes found exclusively in one lib.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2015-02-05 18:56:07 +0900<br />
Author date: 2015-02-05 18:56:07 +0900<br />
Commit id: 8d7215daaefb49b05c9b9d2873877c9d7529c275<br />
Does not use a default table anymore.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2015-02-05 18:09:02 +0900<br />
Author date: 2015-02-05 18:09:02 +0900<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@99073 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
new file mode 100644
index 0000000..48e28d8
--- /dev/null
+++ b/R/private_clonotypes.R
@@ -0,0 +1,28 @@
+private_clonotypes <- function (..., data) {
+
+libs <- c(...)
+otherLibs <- setdiff(colnames(data), libs)
+
+if ( ! is.character(libs) ) stop (
+ "First argument must be a character vector of library names."
+)
+
+if ( ! is.data.frame(data) ) stop (
+ "Second argument must be a data frame of clonotypes."
+)
+
+if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
+ paste("Unknown library: ", libs[ ! libs %in% colnames(data) ],".", sep='', collapse=' ')
+)
+
+clonotypenames <- rownames(data)
+
+# drop=FALSE otherwise rowSums fails when there is only one column.
+
+expressedInLibs <- rowSums(data[, libs , drop=FALSE]) > 0
+absentInOtherLibs <- rowSums(data[, otherLibs, drop=FALSE]) == 0
+
+return(
+ clonotypenames[ expressedInLibs & absentInOtherLibs ]
+)
+}
diff --git a/man/unique_clonotypes.Rd b/man/unique_clonotypes.Rd
index 7e5fff9..2a4d865 100644
--- a/man/unique_clonotypes.Rd
+++ b/man/unique_clonotypes.Rd
@@ -16,10 +16,6 @@ clonotype_table.
\item{data}{The name of the clonotype_table where the data is stored.}
}
-\details{
-Uses the table called \dQuote{clonotypes} by default.
-}
-
\value{
Character vector of clonotype names. Their order follows the original row name
order of the clonotype_table.
</pre>
</div>
change to R/private_clonotypes.R on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_68cdc95e69dd63e8c1d1698036dd7616a982af38/
plessy
2015-02-05T09:56:07Z
2015-02-05T09:56:07Z
<div id="change-68cdc95e69dd63e8c1d1698036dd7616a982af38" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-02-05T09:56:07Z" class="relativedate" title="Thu, 05 Feb 2015 09:56:07 +0000">09:56:07 02/05/15</time></span>
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</span>
</div>
<div class="changelog">
private_clonotpes: a function to list clonotypes found exclusively in one lib.<br />
</div>
<div class="diff">
<pre>
diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
new file mode 100644
index 0000000..48e28d8
--- /dev/null
+++ b/R/private_clonotypes.R
@@ -0,0 +1,28 @@
+private_clonotypes <- function (..., data) {
+
+libs <- c(...)
+otherLibs <- setdiff(colnames(data), libs)
+
+if ( ! is.character(libs) ) stop (
+ "First argument must be a character vector of library names."
+)
+
+if ( ! is.data.frame(data) ) stop (
+ "Second argument must be a data frame of clonotypes."
+)
+
+if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
+ paste("Unknown library: ", libs[ ! libs %in% colnames(data) ],".", sep='', collapse=' ')
+)
+
+clonotypenames <- rownames(data)
+
+# drop=FALSE otherwise rowSums fails when there is only one column.
+
+expressedInLibs <- rowSums(data[, libs , drop=FALSE]) > 0
+absentInOtherLibs <- rowSums(data[, otherLibs, drop=FALSE]) == 0
+
+return(
+ clonotypenames[ expressedInLibs & absentInOtherLibs ]
+)
+}
</pre>
</div>
change to man/unique_clonotypes.Rd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_8d7215daaefb49b05c9b9d2873877c9d7529c275/
plessy
2015-02-05T09:09:02Z
2015-02-05T09:09:02Z
<div id="change-8d7215daaefb49b05c9b9d2873877c9d7529c275" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2015-02-05T09:09:02Z" class="relativedate" title="Thu, 05 Feb 2015 09:09:02 +0000">09:09:02 02/05/15</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Does not use a default table anymore.<br />
</div>
<div class="diff">
<pre>
diff --git a/man/unique_clonotypes.Rd b/man/unique_clonotypes.Rd
index 7e5fff9..2a4d865 100644
--- a/man/unique_clonotypes.Rd
+++ b/man/unique_clonotypes.Rd
@@ -16,10 +16,6 @@ clonotype_table.
\item{data}{The name of the clonotype_table where the data is stored.}
}
-\details{
-Uses the table called \dQuote{clonotypes} by default.
-}
-
\value{
Character vector of clonotype names. Their order follows the original row name
order of the clonotype_table.
</pre>
</div>
change to doc/seaview on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_9211114ac32036c266d542b9d4b2c6b8c7415215/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-12-12T02:33:19Z
2014-12-12T02:33:19Z
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Removed cruft.<br />
</div>
<div class="diff">
<pre>
diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index 3a2b487..bbdd8a2 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -2,8 +2,6 @@
_Page in construction…_
-<span style="background: red; font-family: monospace">TTT</span>
-
[SeaView](http://doua.prabi.fr/software/seaview) is a “multiplatform, graphical
user interface for multiple sequence alignment and molecular phylogeny”. In
addition to the traditional display of nucleotides, it can color the alignment
</pre>
</div>
change to doc/seaview on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_f613975196cc4dd122201f02f3bbd66bec11911c/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-12-12T02:26:06Z
2014-12-12T02:26:06Z
<div id="change-f613975196cc4dd122201f02f3bbd66bec11911c" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="desc"><br />Changed by:</span>
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</span>
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<span class="committype">web</span>
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<span class="changedate"><time datetime="2014-12-12T02:26:06Z" class="relativedate" title="Fri, 12 Dec 2014 02:26:06 +0000">02:26:06 12/12/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
More explanations on how to visualise the alignments with SeaView.<br />
</div>
<div class="diff">
<pre>
diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index 5c99ac4..3a2b487 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -12,13 +12,19 @@ very useful for manual alignemnt of _V_ and _J_ segments.
### Nucleotide view
+J segments must be aligned on the `FGxG` motif, but in the default view it is
+not very obvious to see. Switch to the codon view or the aminoacid view.
+
[[!img SeaView_nucleotides.png alt="SeaView displaying colored nucleotides."]]
### Codon view
+Here, the `FGxG` motif stands out like for example “<span style="background: red; font-family: monospace">TTC</span><span style="background: lime; font-family: monospace">GGT</span><span style="background: olive; font-family: monospace">CAT</span><span style="background: lime; font-family: monospace">GGA</span>”. This mode is very useful for finding the relevant reading frame, by adding or removing gaps before the first nucleotide.
+
[[!img SeaView_codons.png alt="SeaView displaying colored codons."]]
### Aminoacid view
-[[!img SeaView_aminoacids.png alt="SeaView displaying colored aminoacids translated from the DNA sequences."]]
+This mode is very useful for aligning in-frame sequences, checking the final alignment, and spotting easily the stop codons in pseudogenised segments.
+[[!img SeaView_aminoacids.png alt="SeaView displaying colored aminoacids translated from the DNA sequences."]]
</pre>
</div>
change to doc/seaview on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_09dec74eb038ffb6f43a7d4b1162fd9ed56a1d32/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-12-12T02:18:01Z
2014-12-12T02:18:01Z
<div id="change-09dec74eb038ffb6f43a7d4b1162fd9ed56a1d32" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="desc"><br />Changed by:</span>
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<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
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<pre>
diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index b40f1c6..5c99ac4 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -2,6 +2,8 @@
_Page in construction…_
+<span style="background: red; font-family: monospace">TTT</span>
+
[SeaView](http://doua.prabi.fr/software/seaview) is a “multiplatform, graphical
user interface for multiple sequence alignment and molecular phylogeny”. In
addition to the traditional display of nucleotides, it can color the alignment
</pre>
</div>
change to doc/seaview on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_15c48a5de6cddc546c7bcac0013b00d94e41f5cf/
plessy
2014-12-12T02:00:16Z
2014-12-12T02:00:16Z
<div id="change-15c48a5de6cddc546c7bcac0013b00d94e41f5cf" class="metadata">
<span class="desc"><br />Changed pages:</span>
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</span>
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<div class="changelog">
Syntax correction.<br />
</div>
<div class="diff">
<pre>
diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index c0fb06e..b40f1c6 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -14,7 +14,7 @@ very useful for manual alignemnt of _V_ and _J_ segments.
### Codon view
-[[!img SeaView_codons.png alt="SeaView displaying colored codons."]
+[[!img SeaView_codons.png alt="SeaView displaying colored codons."]]
### Aminoacid view
</pre>
</div>
change to references/README on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_72f5a9c6f5e1ad3adc736e954aa20ae6b3030b23/
https://launchpad.net/~plessy
2014-12-12T01:59:10Z
2014-12-12T01:59:10Z
<div id="change-72f5a9c6f5e1ad3adc736e954aa20ae6b3030b23" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
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<span class="desc"><br /></span>
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</span>
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<div class="changelog">
Link to the SeaView page.<br />
</div>
<div class="diff">
<pre>
diff --git a/references/README.mdwn b/references/README.mdwn
index 4f98128..8f7211a 100644
--- a/references/README.mdwn
+++ b/references/README.mdwn
@@ -10,7 +10,7 @@ extracted with the command `make gb2fa`, wich uses the the [extractfeat][]
program of the EMBOSS package.
This directory contains *V* and *J* segments aligned on conserved motifs in the
-files [[V.fa]] and [[J.fa]]. These alignments were made by hand using [SeaView][] and
+files [[V.fa]] and [[J.fa]]. These alignments were made by hand using [[SeaView|doc/seaview]] and
may need to be revised when the reference sequences change.
[Mmus_TRA]: http://www.ncbi.nlm.nih.gov/nuccore/NG_007044 (Mus musculus T cell receptor alpha delta locus (Tcra/tcrd@) on chromosome 14)
</pre>
</div>
change to doc/seaview doc/seaview/SeaView_aminoacids.png doc/seaview/SeaView_codons.png doc/seaview/SeaView_nucleotides.png on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_0fbe7a7777415f9575bba736fc76c8a008d3f5f4/
plessy
2014-12-12T01:52:12Z
2014-12-12T01:52:12Z
<div id="change-0fbe7a7777415f9575bba736fc76c8a008d3f5f4" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=doc/seaview.mdwn;h=c0fb06ee9859b91b012a82abedaf021f704dc729;hp=0000000000000000000000000000000000000000;hb=0fbe7a7777415f9575bba736fc76c8a008d3f5f4;hpb=0beb9441c2cb369ace5bb20b119add5358e22078" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=doc%2Fseaview&do=goto" rel="nofollow">doc/seaview</a>
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=doc/seaview/SeaView_aminoacids.png;h=929bf6fff059b202a766435436dd061a04e26dc0;hp=0000000000000000000000000000000000000000;hb=0fbe7a7777415f9575bba736fc76c8a008d3f5f4;hpb=0beb9441c2cb369ace5bb20b119add5358e22078" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=doc%2Fseaview%2FSeaView_aminoacids.png&do=goto" rel="nofollow">doc/seaview/SeaView aminoacids.png</a>
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=doc/seaview/SeaView_codons.png;h=3d7ebd44408e6831f855b6fe50f972f3c5a5917d;hp=0000000000000000000000000000000000000000;hb=0fbe7a7777415f9575bba736fc76c8a008d3f5f4;hpb=0beb9441c2cb369ace5bb20b119add5358e22078" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=doc%2Fseaview%2FSeaView_codons.png&do=goto" rel="nofollow">doc/seaview/SeaView codons.png</a>
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=doc/seaview/SeaView_nucleotides.png;h=3d2bd236fbf3ed59fc24d8b866aae94e00ebada0;hp=0000000000000000000000000000000000000000;hb=0fbe7a7777415f9575bba736fc76c8a008d3f5f4;hpb=0beb9441c2cb369ace5bb20b119add5358e22078" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=doc%2Fseaview%2FSeaView_nucleotides.png&do=goto" rel="nofollow">doc/seaview/SeaView nucleotides.png</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=plessy&do=goto" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-12-12T01:52:12Z" class="relativedate" title="Fri, 12 Dec 2014 01:52:12 +0000">01:52:12 12/12/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Documenting the different alignment modes of SeaView.<br />
</div>
<div class="diff">
<pre>
diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
new file mode 100644
index 0000000..c0fb06e
--- /dev/null
+++ b/doc/seaview.mdwn
@@ -0,0 +1,22 @@
+# Alignment of V and J segements with SeaView.
+
+_Page in construction…_
+
+[SeaView](http://doua.prabi.fr/software/seaview) is a “multiplatform, graphical
+user interface for multiple sequence alignment and molecular phylogeny”. In
+addition to the traditional display of nucleotides, it can color the alignment
+by codons, or display the DNA sequence translated as protein. This makes it
+very useful for manual alignemnt of _V_ and _J_ segments.
+
+### Nucleotide view
+
+[[!img SeaView_nucleotides.png alt="SeaView displaying colored nucleotides."]]
+
+### Codon view
+
+[[!img SeaView_codons.png alt="SeaView displaying colored codons."]
+
+### Aminoacid view
+
+[[!img SeaView_aminoacids.png alt="SeaView displaying colored aminoacids translated from the DNA sequences."]]
+
diff --git a/doc/seaview/SeaView_aminoacids.png b/doc/seaview/SeaView_aminoacids.png
new file mode 100644
index 0000000..929bf6f
Binary files /dev/null and b/doc/seaview/SeaView_aminoacids.png differ
diff --git a/doc/seaview/SeaView_codons.png b/doc/seaview/SeaView_codons.png
new file mode 100644
index 0000000..3d7ebd4
Binary files /dev/null and b/doc/seaview/SeaView_codons.png differ
diff --git a/doc/seaview/SeaView_nucleotides.png b/doc/seaview/SeaView_nucleotides.png
new file mode 100644
index 0000000..3d2bd23
Binary files /dev/null and b/doc/seaview/SeaView_nucleotides.png differ
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5eb2fe609da4888aa2a2f3c2502e1a3f461d73b0/
https://launchpad.net/~plessy
2014-12-12T01:37:17Z
2014-12-12T01:37:17Z
<div id="change-5eb2fe609da4888aa2a2f3c2502e1a3f461d73b0" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
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<span class="committype">web</span>
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<span class="changedate"><time datetime="2014-12-12T01:37:17Z" class="relativedate" title="Fri, 12 Dec 2014 01:37:17 +0000">01:37:17 12/12/14</time></span>
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</span>
</div>
<div class="changelog">
Link to new Bioconductor release.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index f5ecc8b..7099cc2 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -45,6 +45,8 @@ to try alternative solutions, you can have a look at
### Recent news
+ * October 2014: New stable version [1.4](http://www.bioconductor.org/packages/3.0/bioc/html/clonotypeR.html)
+ released on Bioconductor.
* 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.
* March 2014: New stable version [1.2](http://www.bioconductor.org/packages/2.14/bioc/html/clonotypeR.html)
released on Bioconductor.
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5528d5d562cbcb746b38530c4af1c14918c21544/
bioc-sync
2014-10-13T22:07:54Z
2014-10-13T22:07:54Z
<div id="change-5528d5d562cbcb746b38530c4af1c14918c21544" class="metadata">
<span class="desc"><br />Changed pages:</span>
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 1 commit.<br />
Commit information:<br />
SVN Revision number: 95443<br />
Commit message:<br />
Bumping versions after creating 3.0 release branch.<br />
Committed by d.tenenbaum<br />
Committed at: 2014-10-13T21:47:41.382147Z<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index ea7a4e3..f304114 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.4.0
+Version: 1.5.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5e276f8999ba8c83cfa09b4f0a58bd2c1e047a47/
d.tenenbaum
2014-10-13T21:47:41Z
2014-10-13T21:47:41Z
<div id="change-5e276f8999ba8c83cfa09b4f0a58bd2c1e047a47" class="metadata">
<span class="desc"><br />Changed pages:</span>
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</span>
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Bumping versions after creating 3.0 release branch.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@95443 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index ea7a4e3..f304114 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.4.0
+Version: 1.5.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_e26c2eeb16d377f4c447d54c1c8bb23c09f5ee03/
bioc-sync
2014-10-13T21:46:18Z
2014-10-13T21:46:18Z
<div id="change-e26c2eeb16d377f4c447d54c1c8bb23c09f5ee03" class="metadata">
<span class="desc"><br />Changed pages:</span>
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 1 commit.<br />
Commit information:<br />
SVN Revision number: 95439<br />
Commit message:<br />
Bump package versions prior to creating the 3.0 branch.<br />
Committed by d.tenenbaum<br />
Committed at: 2014-10-13T21:38:33.867451Z<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 1ef9e8b..ea7a4e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.2
+Version: 1.4.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_aae491b43b075246bcedf235a35de3f23795bd19/
d.tenenbaum
2014-10-13T21:38:33Z
2014-10-13T21:38:33Z
<div id="change-aae491b43b075246bcedf235a35de3f23795bd19" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=ea7a4e357a8aa7b4bae6dd67fa64db1859fdcda0;hp=1ef9e8bfab151c4d49ceda3a2b09d86cd9d10ea5;hb=aae491b43b075246bcedf235a35de3f23795bd19;hpb=b677a8e65eaa6c2638c9dd8b92eba608e4e582f7" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
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Bump package versions prior to creating the 3.0 branch.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@95439 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 1ef9e8b..ea7a4e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.2
+Version: 1.4.0
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to index on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_3d116c0cda96e335ecd141f4a027516d86322ec0/
plessy
2014-09-25T09:30:20Z
2014-09-25T09:30:20Z
<div id="change-3d116c0cda96e335ecd141f4a027516d86322ec0" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=index.mdwn;h=f5ecc8ba9750750de65f1800c639fcb0a6323dfb;hp=357e7b9bd225c614eb699638399b883cd6cf7a47;hb=3d116c0cda96e335ecd141f4a027516d86322ec0;hpb=4e400f7eabe5b5fbe79585f58bf33a98b92384ca" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=index&do=goto" rel="nofollow">index</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=plessy&do=goto" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
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<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T09:30:20Z" class="relativedate" title="Thu, 25 Sep 2014 09:30:20 +0000">09:30:20 09/25/14</time></span>
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</span>
</div>
<div class="changelog">
Release version 1.3.2.<br />
</div>
<div class="diff">
<pre>
diff --git a/index.mdwn b/index.mdwn
index 357e7b9..f5ecc8b 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -45,6 +45,7 @@ to try alternative solutions, you can have a look at
### Recent news
+ * 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.
* March 2014: New stable version [1.2](http://www.bioconductor.org/packages/2.14/bioc/html/clonotypeR.html)
released on Bioconductor.
* 11 December 2013: Version 1.1.3 adding a `long` option to `yassai_identifier`, solving
</pre>
</div>
change to ChangeLog DESCRIPTION NEWS vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_b677a8e65eaa6c2638c9dd8b92eba608e4e582f7/
c.plessy
2014-09-25T09:21:03Z
2014-09-25T09:21:03Z
<div id="change-b677a8e65eaa6c2638c9dd8b92eba608e4e582f7" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<div class="changelog">
Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 4 commits.<br />
Commit information:<br />
Commit id: 8a1934044597a69bacf2acd3594c3183661d6e7f<br />
Version 1.3.2, release candidate.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 18:20:39 +0900<br />
Author date: 2014-09-25 18:20:39 +0900<br />
Commit id: 46cc1439ff43464b15a90efe222afe59a419cd2c<br />
Upcoming version 1.4.0: no major changes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 18:17:00 +0900<br />
Author date: 2014-09-25 18:17:00 +0900<br />
Commit id: ae5e044a195fdc86dd0af7bdfddf27fb37dab0f4<br />
Uppercase final letter in 'clonotypeR'.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 13:33:29 +0900<br />
Author date: 2014-09-25 13:33:29 +0900<br />
Commit id: 0f724d3a35d432366a5b41fc7514af1d89da506a<br />
Corrected a typo.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 13:31:40 +0900<br />
Author date: 2014-09-25 13:31:40 +0900<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@94519 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/ChangeLog b/ChangeLog
index 8c90a52..06e2de0 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+2014-09-25 Charles Plessy <plessy@riken.jp>
+ * Version 1.3.2
+ * Import “methods” instead of depending on.
+ * Corrected typos.
+
2014-04-08 Charles Plessy <plessy@riken.jp>
* Version 1.1.6
* Transfer “NEWS” to ChangeLog and add release notes to “NEWS”.
@@ -8,7 +13,7 @@
2014-03-05 Bioc admins
* Version 1.1.4.
- * Change biocviews to “Sequencing”,
+ * Change biocviews to “Sequencing”.
2013-12-11 Charles Plessy <plessy@riken>
* Committed 1.1.3 to Bioconductor.
diff --git a/DESCRIPTION b/DESCRIPTION
index 3370138..1ef9e8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.1
+Version: 1.3.2
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
diff --git a/NEWS b/NEWS
index e8067a7..4b9b4a2 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.4.0
+
+BUG FIXES
+
+ o Minor packaging corrections (NAMESPACE, etc.).
+
Changes in version 1.2.0
NEW FEATURES
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 32f4fe7..8679d56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -126,13 +126,13 @@ of the display).
### Detection of V segments
-Run the command `clonotyper detect A.fastq` in the same directory as a copy of
+Run the command `clonotypeR detect A.fastq` in the same directory as a copy of
the file `A.fastq`.
The result is stored in a temporary directory called `extraction_files`, that
will be created if it does not already exist.
-`clonotyper detect` compares the sequences to the reference V segments using
+`clonotypeR detect` compares the sequences to the reference V segments using
BWA, and produces output like the following.
[bsw2_aln] read 2000 sequences/pairs (843395 bp)...
@@ -146,13 +146,13 @@ pairs in total. There were 167 reference V segments, and the version number of
BWA was `0.6.2-r126`. The whole process took less than 10 seconds.
Process the example libraries `B` and `C` similarly with the commands
-`clonotyper detect C.fastq` and `clonotyper detect C.fastq`.
+`clonotypeR detect B.fastq` and `clonotypeR detect C.fastq`.
### Extraction of CDR3 regions
-Run the command `clonotyper extract A` in the same directory as where you ran
-`clonotyper detect A.fastq`. The result is a table stored in a directory
+Run the command `clonotypeR extract A` in the same directory as where you ran
+`clonotypeR detect A.fastq`. The result is a table stored in a directory
called `clonotypes`, that will be created if it does not already exist.
The output is quite voluminous, and indicates which *V* / *J* combinations are
</pre>
</div>
change to ChangeLog DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_8a1934044597a69bacf2acd3594c3183661d6e7f/
plessy
2014-09-25T09:20:39Z
2014-09-25T09:20:39Z
<div id="change-8a1934044597a69bacf2acd3594c3183661d6e7f" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="changedate"><time datetime="2014-09-25T09:20:39Z" class="relativedate" title="Thu, 25 Sep 2014 09:20:39 +0000">09:20:39 09/25/14</time></span>
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</span>
</div>
<div class="changelog">
Version 1.3.2, release candidate.<br />
</div>
<div class="diff">
<pre>
diff --git a/ChangeLog b/ChangeLog
index 8c90a52..06e2de0 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+2014-09-25 Charles Plessy <plessy@riken.jp>
+ * Version 1.3.2
+ * Import “methods” instead of depending on.
+ * Corrected typos.
+
2014-04-08 Charles Plessy <plessy@riken.jp>
* Version 1.1.6
* Transfer “NEWS” to ChangeLog and add release notes to “NEWS”.
@@ -8,7 +13,7 @@
2014-03-05 Bioc admins
* Version 1.1.4.
- * Change biocviews to “Sequencing”,
+ * Change biocviews to “Sequencing”.
2013-12-11 Charles Plessy <plessy@riken>
* Committed 1.1.3 to Bioconductor.
diff --git a/DESCRIPTION b/DESCRIPTION
index 3370138..1ef9e8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.1
+Version: 1.3.2
Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to NEWS on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_46cc1439ff43464b15a90efe222afe59a419cd2c/
plessy
2014-09-25T09:17:00Z
2014-09-25T09:17:00Z
<div id="change-46cc1439ff43464b15a90efe222afe59a419cd2c" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=NEWS;h=4b9b4a20e9fd1d0ec50014da406a7eacf5336780;hp=e8067a7c2b7ab58bca1c6c0c3292bcb6106f1211;hb=46cc1439ff43464b15a90efe222afe59a419cd2c;hpb=ae5e044a195fdc86dd0af7bdfddf27fb37dab0f4" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=NEWS&do=goto" rel="nofollow">NEWS</a>
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</span>
</div>
<div class="changelog">
Upcoming version 1.4.0: no major changes.<br />
</div>
<div class="diff">
<pre>
diff --git a/NEWS b/NEWS
index e8067a7..4b9b4a2 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.4.0
+
+BUG FIXES
+
+ o Minor packaging corrections (NAMESPACE, etc.).
+
Changes in version 1.2.0
NEW FEATURES
</pre>
</div>
change to Bugs/Does_not_work_with_EMBOSS_6.6.0. on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_8e3da047e5f7a8c6e5a1a9d5d614d78ffbd7dc22/
plessy
2014-09-25T08:58:44Z
2014-09-25T08:58:44Z
<div id="change-8e3da047e5f7a8c6e5a1a9d5d614d78ffbd7dc22" class="metadata">
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</span>
</div>
<div class="changelog">
Correct version number of EMBOSS.<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
index bbbe652..fdea6b3 100644
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -1,4 +1,4 @@
-In EMBOSS 6.6.6, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.
+In EMBOSS 6.6.0, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.
<pre>
echo -e '>A\nAAAAAA' > test-1.fa
</pre>
</div>
change to scripts/VJsplit on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_71a29d82285dd44e8eae4aa20da50db30b2196fa/
plessy
2014-09-25T08:56:25Z
2014-09-25T08:56:25Z
<div id="change-71a29d82285dd44e8eae4aa20da50db30b2196fa" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=scripts/VJsplit;h=b7502ea72a94cabdd31d13d68d3f5e17c61a2a11;hp=4b23919902c58e233c0b8fd2548036581cb027ad;hb=71a29d82285dd44e8eae4aa20da50db30b2196fa;hpb=f879ea04e5f5723b8d473553ff02925515bfcfd0" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=scripts%2FVJsplit&do=goto" rel="nofollow">scripts/VJsplit</a>
</span>
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
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<span class="changedate"><time datetime="2014-09-25T08:56:25Z" class="relativedate" title="Thu, 25 Sep 2014 08:56:25 +0000">08:56:25 09/25/14</time></span>
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</span>
</div>
<div class="changelog">
Suppress warnings in vectorscript.<br />
Since EMBOSS 6.6.0, vectorscript emits a warning when no matches are<br />
found, which is annoying here. Better solutions are welcome.<br />
</div>
<div class="diff">
<pre>
diff --git a/scripts/VJsplit b/scripts/VJsplit
index 4b23919..b7502ea 100755
--- a/scripts/VJsplit
+++ b/scripts/VJsplit
@@ -72,7 +72,7 @@ do
fi
echo -ne "\t$J_NAME\t" 1>&2
J_SEQ=$(seqret -filter $CLONOTYPER_REFERENCE/${J_LIB}-FGxG.fa:$J_NAME[:20] raw:stdout)
- vectorstrip -auto \
+ EMBOSS_WARNING=FALSE vectorstrip -auto \
-readfile N \
-mismatch $VS_MISMATCH \
-blinker $(seqret -filter $CLONOTYPER_REFERENCE/${J_LIB}-FGxG.fa:$J_NAME[:20] raw:stdout) \
</pre>
</div>
change to vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_f879ea04e5f5723b8d473553ff02925515bfcfd0/
plessy
2014-09-25T08:42:56Z
2014-09-25T08:42:56Z
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Merge branch 'bioc'<br />
</div>
change to Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_ on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_6c70226d09ab121b3173300bab6fc7f04c89c745/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-09-25T08:40:46Z
2014-09-25T08:40:46Z
<div id="change-6c70226d09ab121b3173300bab6fc7f04c89c745" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn;h=7b7fef9f33bde521691da1800de00dbd20e1e4d2;hp=1648dceb3ba23225691bf9a6e55d17ea9071671b;hb=6c70226d09ab121b3173300bab6fc7f04c89c745;hpb=cbad9feec7e77e816bbcc628fb78ed2f924670c5" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FIncorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_&do=goto" rel="nofollow">Bugs/Incorrect identifiers when V-J boundary is a codon boundary </a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:40:46Z" class="relativedate" title="Thu, 25 Sep 2014 08:40:46 +0000">08:40:46 09/25/14</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?rev=6c70226d09ab121b3173300bab6fc7f04c89c745&do=revert" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Shortcut to commit.<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
index 1648dce..7b7fef9 100644
--- a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
+++ b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
@@ -3,7 +3,7 @@
[1] "tg.integer(0)A2A61L13"
</pre>
-[[Done]] in `2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd`, by return an empty chain instead of `integer(0)` when receiving an empty chain.
+[[Done]] in [[!commit 2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd]], by return an empty chain instead of `integer(0)` when receiving an empty chain.
Result after correction:
</pre>
</div>
change to Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier. on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_cbad9feec7e77e816bbcc628fb78ed2f924670c5/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-09-25T08:40:24Z
2014-09-25T08:40:24Z
<div id="change-cbad9feec7e77e816bbcc628fb78ed2f924670c5" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn;h=e8138031aba34732237e5cf8517e6f6a72655044;hp=7cdfc9170bcfebe1a44aac8afce7f2a8ff0a754a;hb=cbad9feec7e77e816bbcc628fb78ed2f924670c5;hpb=74cfea0cee6df4156229c959eab2e1dcddbaefbe" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FClonotype_that_takes_ages_for_calculating_the_Yassai_identifier.&do=goto" rel="nofollow">Bugs/Clonotype that takes ages for calculating the Yassai identifier.</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:40:24Z" class="relativedate" title="Thu, 25 Sep 2014 08:40:24 +0000">08:40:24 09/25/14</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?rev=cbad9feec7e77e816bbcc628fb78ed2f924670c5&do=revert" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Shortcut to commit.<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
index 7cdfc91..e813803 100644
--- a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
+++ b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
@@ -45,7 +45,7 @@ TRAV14N-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This triggered an infinite loop when calling `is.germline()`.
-[[Done]] in `42ab98729c5c77462b5929b00ee973074ae4c1c7`.
+[[Done]] in [[!commit 42ab98729c5c77462b5929b00ee973074ae4c1c7]].
Now the function should return as in the following example.
</pre>
</div>
change to Bugs/Does_not_work_with_EMBOSS_6.6.0. on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_74cfea0cee6df4156229c959eab2e1dcddbaefbe/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-09-25T08:38:54Z
2014-09-25T08:38:54Z
<div id="change-74cfea0cee6df4156229c959eab2e1dcddbaefbe" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn;h=bbbe65241e7705bdbebd88d717e0fcd32b0b31e2;hp=45abb7dda212a3092c1d70885beaed3138cd54dc;hb=74cfea0cee6df4156229c959eab2e1dcddbaefbe;hpb=da67ea6ce7958e4fc5f6c62cf910e8454902340b" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FDoes_not_work_with_EMBOSS_6.6.0.&do=goto" rel="nofollow">Bugs/Does not work with EMBOSS 6.6.0.</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:38:54Z" class="relativedate" title="Thu, 25 Sep 2014 08:38:54 +0000">08:38:54 09/25/14</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?rev=74cfea0cee6df4156229c959eab2e1dcddbaefbe&do=revert" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Edit rebased commit ID.<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
index 45abb7d..bbbe652 100644
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -19,4 +19,4 @@ seqret test-1.fa:A stdout
See also <http://lists.open-bio.org/pipermail/emboss/2014-June/008983.html>
-[[Done]] with the following workaround: the directory `references/V` was renamed `references/V-C` in [[!commit 055b6807d3f0e6fc6dda58f5699c6ac34fbc89c2]].
+[[Done]] with the following workaround: the directory `references/V` was renamed `references/V-C` in [[!commit 125524131bd57c084ee39374054b73784e6ae929]].
</pre>
</div>
change to shortcuts on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_a8d980bf1df8964a8a01545b6ff3760af0484d64/
plessy
2014-09-25T08:33:29Z
2014-09-25T08:33:29Z
<div id="change-a8d980bf1df8964a8a01545b6ff3760af0484d64" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=shortcuts.mdwn;h=0cd4821d77131cff488e96370b33020367859eea;hp=ca529c296b64e9eb34f884c5a1595365ea41cca6;hb=a8d980bf1df8964a8a01545b6ff3760af0484d64;hpb=00c30bf6c6dacc79edc6d86a5c684c68a6cfc0f2" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=shortcuts&do=goto" rel="nofollow">shortcuts</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=plessy&do=goto" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:33:29Z" class="relativedate" title="Thu, 25 Sep 2014 08:33:29 +0000">08:33:29 09/25/14</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?rev=a8d980bf1df8964a8a01545b6ff3760af0484d64&do=revert" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Add a new shortcut for commits.<br />
</div>
<div class="diff">
<pre>
diff --git a/shortcuts.mdwn b/shortcuts.mdwn
index ca529c2..0cd4821 100644
--- a/shortcuts.mdwn
+++ b/shortcuts.mdwn
@@ -64,6 +64,8 @@ This page controls what shortcut links the wiki supports.
* [[!shortcut name=freebsdwiki url="http://wiki.freebsd.org/%s"]]
* [[!shortcut name=hackage url="http://hackage.haskell.org/package/%s"]]
+* [[!shortcut name=commit url="http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s"]]
+
To add a new shortcut, use the `shortcut`
[[ikiwiki/directive]]. In the url, "%s" is replaced with the
text passed to the named shortcut, after [[!wikipedia url_encoding]]
</pre>
</div>
change to shortcuts on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_00c30bf6c6dacc79edc6d86a5c684c68a6cfc0f2/
plessy
2014-09-25T08:32:32Z
2014-09-25T08:32:32Z
<div id="change-00c30bf6c6dacc79edc6d86a5c684c68a6cfc0f2" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=shortcuts.mdwn;h=ca529c296b64e9eb34f884c5a1595365ea41cca6;hp=0000000000000000000000000000000000000000;hb=00c30bf6c6dacc79edc6d86a5c684c68a6cfc0f2;hpb=125524131bd57c084ee39374054b73784e6ae929" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=shortcuts&do=goto" rel="nofollow">shortcuts</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=plessy&do=goto" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:32:32Z" class="relativedate" title="Thu, 25 Sep 2014 08:32:32 +0000">08:32:32 09/25/14</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?rev=00c30bf6c6dacc79edc6d86a5c684c68a6cfc0f2&do=revert" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Ikiwiki's shortcuts page.<br />
</div>
<div class="diff">
<pre>
diff --git a/shortcuts.mdwn b/shortcuts.mdwn
new file mode 100644
index 0000000..ca529c2
--- /dev/null
+++ b/shortcuts.mdwn
@@ -0,0 +1,83 @@
+[[!if test="enabled(shortcut)"
+ then="This wiki has shortcuts **enabled**."
+ else="This wiki has shortcuts **disabled**."]]
+
+Some examples of using shortcuts include:
+
+ \[[!google foo]]
+ \[[!wikipedia War_of_1812]]
+ \[[!debbug 12345]]
+ Check the \[[!google ikiwiki desc="google search for %s"]].
+
+This page controls what shortcut links the wiki supports.
+
+* [[!shortcut name=google url="https://encrypted.google.com/search?q=%s"]]
+* [[!shortcut name=archive url="http://web.archive.org/*/%S"]]
+* [[!shortcut name=gmap url="https://maps.google.com/maps?q=%s"]]
+* [[!shortcut name=gmsg url="https://groups.google.com/groups?selm=%s"]]
+* [[!shortcut name=wikipedia url="https://en.wikipedia.org/wiki/%W"]]
+* [[!shortcut name=wikitravel url="https://wikitravel.org/en/%s"]]
+* [[!shortcut name=wiktionary url="https://en.wiktionary.org/wiki/%s"]]
+* [[!shortcut name=debbug url="http://bugs.debian.org/%S" desc="Debian bug #%s"]]
+* [[!shortcut name=deblist url="https://lists.debian.org/debian-%s" desc="debian-%s@lists.debian.org"]]
+* [[!shortcut name=debpkg url="http://packages.debian.org/%s"]]
+* [[!shortcut name=debpkgsid url="http://packages.debian.org/sid/%s"]]
+* [[!shortcut name=debpts url="http://packages.qa.debian.org/%s"]]
+* [[!shortcut name=debmsg url="https://lists.debian.org/msgid-search/%s"]]
+* [[!shortcut name=debrt url="https://rt.debian.org/Ticket/Display.html?id=%s"]]
+* [[!shortcut name=debss url="http://snapshot.debian.org/package/%s/"]]
+ * Usage: `\[[!debss package]]` or `\[[!debss package/version]]`. See <http://snapshot.debian.org/> for details.
+* [[!shortcut name=debwiki url="https://wiki.debian.org/%S"]]
+* [[!shortcut name=fdobug url="https://bugs.freedesktop.org/show_bug.cgi?id=%s" desc="freedesktop.org bug #%s"]]
+* [[!shortcut name=fdolist url="http://lists.freedesktop.org/mailman/listinfo/%s" desc="%s@lists.freedesktop.org"]]
+* [[!shortcut name=gnomebug url="https://bugzilla.gnome.org/show_bug.cgi?id=%s" desc="GNOME bug #%s"]]
+* [[!shortcut name=linuxbug url="https://bugzilla.kernel.org/show_bug.cgi?id=%s" desc="Linux bug #%s"]]
+* [[!shortcut name=mozbug url="https://bugzilla.mozilla.org/show_bug.cgi?id=%s" desc="Mozilla bug #%s"]]
+* [[!shortcut name=gnulist url="https://lists.gnu.org/mailman/listinfo/%s" desc="%s@gnu.org"]]
+* [[!shortcut name=marcmsg url="http://marc.info/?i=%s"]]
+* [[!shortcut name=marclist url="http://marc.info/?l=%s"]]
+* [[!shortcut name=gmane url="http://dir.gmane.org/gmane.%s" desc="gmane.%s"]]
+* [[!shortcut name=gmanemsg url="http://mid.gmane.org/%s"]]
+* [[!shortcut name=cpan url="http://search.cpan.org/search?mode=dist&query=%s"]]
+* [[!shortcut name=ctan url="http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=%s"]]
+* [[!shortcut name=hoogle url="http://haskell.org/hoogle/?q=%s"]]
+* [[!shortcut name=iki url="http://ikiwiki.info/%S/"]]
+* [[!shortcut name=ljuser url="http://%s.livejournal.com/"]]
+* [[!shortcut name=rfc url="https://www.ietf.org/rfc/rfc%s.txt" desc="RFC %s"]]
+* [[!shortcut name=c2 url="http://c2.com/cgi/wiki?%s"]]
+* [[!shortcut name=meatballwiki url="http://www.usemod.com/cgi-bin/mb.pl?%s"]]
+* [[!shortcut name=emacswiki url="http://www.emacswiki.org/cgi-bin/wiki/%s"]]
+* [[!shortcut name=haskellwiki url="http://haskell.org/haskellwiki/%s"]]
+* [[!shortcut name=dict url="http://www.dict.org/bin/Dict?Form=Dict1&Strategy=*&Database=*&Query=%s"]]
+* [[!shortcut name=imdb url="http://imdb.com/find?q=%s"]]
+* [[!shortcut name=gpg url="http://pgpkeys.mit.edu:11371/pks/lookup?op=vindex&exact=on&search=0x%s"]]
+* [[!shortcut name=perldoc url="http://perldoc.perl.org/search.html?q=%s"]]
+* [[!shortcut name=whois url="http://reports.internic.net/cgi/whois?whois_nic=%s&type=domain"]]
+* [[!shortcut name=cve url="https://cve.mitre.org/cgi-bin/cvename.cgi?name=%s"]]
+* [[!shortcut name=flickr url="https://secure.flickr.com/photos/%s"]]
+* [[!shortcut name=man url="http://manpages.debian.org/%s"]]
+* [[!shortcut name=ohloh url="https://www.ohloh.net/p/%s"]]
+* [[!shortcut name=cpanrt url="https://rt.cpan.org/Ticket/Display.html?id=%s" desc="CPAN RT#%s"]]
+* [[!shortcut name=novellbug url="https://bugzilla.novell.com/show_bug.cgi?id=%s" desc="bug %s"]]
+* [[!shortcut name=ubupkg url="http://packages.ubuntu.com/%s"]]
+* [[!shortcut name=mozillazinekb url="http://kb.mozillazine.org/%s"]]
+* [[!shortcut name=freebsdwiki url="http://wiki.freebsd.org/%s"]]
+* [[!shortcut name=hackage url="http://hackage.haskell.org/package/%s"]]
+
+To add a new shortcut, use the `shortcut`
+[[ikiwiki/directive]]. In the url, "%s" is replaced with the
+text passed to the named shortcut, after [[!wikipedia url_encoding]]
+it, and '%S' is replaced with the raw, non-encoded text.
+Additionally, `%W` is replaced with the text encoded just right for
+Wikipedia. The optional `desc` parameter controls the description of
+the link.
+
+Remember that the `name` you give the shortcut will become a new
+[[ikiwiki/directive]]. Avoid using a `name` that conflicts
+with an existing directive. These directives also accept a `desc`
+parameter that will override the one provided at definition time.
+
+If you come up with a shortcut that you think others might find useful,
+consider contributing it to the [shortcuts page on the ikiwiki
+wiki](http://ikiwiki.info/shortcuts/), so that future versions of
+ikiwiki will include your shortcut in the standard underlay.
</pre>
</div>
change to Bugs/Does_not_work_with_EMBOSS_6.6.0. on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_2fdcadd0b912d8d31c5fd95b1d04e30013a05dc2/
http://population-transcriptomics.org/People/Charles_Plessy/
2014-09-25T08:31:00Z
2014-09-25T08:31:00Z
<div id="change-2fdcadd0b912d8d31c5fd95b1d04e30013a05dc2" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn;h=45abb7dda212a3092c1d70885beaed3138cd54dc;hp=c95cbe81b47eeca68d2d67c6eee610dce2ea9363;hb=2fdcadd0b912d8d31c5fd95b1d04e30013a05dc2;hpb=de449193bde6e56a204d3b12c7f4e489a780e4b2" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FDoes_not_work_with_EMBOSS_6.6.0.&do=goto" rel="nofollow">Bugs/Does not work with EMBOSS 6.6.0.</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://population-transcriptomics.org/People/Charles_Plessy/" rel="nofollow">Charles_Plessy [population-transcriptomics.org/People]</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:31:00Z" class="relativedate" title="Thu, 25 Sep 2014 08:31:00 +0000">08:31:00 09/25/14</time></span>
<span class="desc"><br /></span>
<span class="revert">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?rev=2fdcadd0b912d8d31c5fd95b1d04e30013a05dc2&do=revert" title="revert" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/revert.png" alt="revert" /></a>
</span>
</div>
<div class="changelog">
Workaround: rename V directory to V-C.<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
index c95cbe8..45abb7d 100644
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -1,4 +1,4 @@
-The reason is the following bug in EMBOSS.
+In EMBOSS 6.6.6, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.
<pre>
echo -e '>A\nAAAAAA' > test-1.fa
@@ -16,3 +16,7 @@ seqret test-1.fa:A stdout
# Error: Unable to read sequence 'test-1.fa:A'
# Died: seqret terminated: Bad value for '-sequence' and no prompt
</pre>
+
+See also <http://lists.open-bio.org/pipermail/emboss/2014-June/008983.html>
+
+[[Done]] with the following workaround: the directory `references/V` was renamed `references/V-C` in [[!commit 055b6807d3f0e6fc6dda58f5699c6ac34fbc89c2]].
</pre>
</div>
change to doc/examples/with_test_data html_doc/clonotypeR.html references/Makefile references/V-C/index.amb references/V-C/index.ann references/V-C/index.bwt references/V-C/index.pac references/V-C/index.sa references/V/index.amb references/V/index.ann on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_125524131bd57c084ee39374054b73784e6ae929/
plessy
2014-09-25T08:10:25Z
2014-09-25T08:10:25Z
<div id="change-125524131bd57c084ee39374054b73784e6ae929" class="metadata">
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...
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T08:10:25Z" class="relativedate" title="Thu, 25 Sep 2014 08:10:25 +0000">08:10:25 09/25/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Moved references/V to references/V-C. This solves an ambiguity in seqret.<br />
Closes: http://clonotyper.branchable.com/Bugs/Does_not_work_with_EMBOSS_6.6.0./<br />
</div>
<div class="diff">
<pre>
diff --git a/doc/examples/with_test_data.mdwn b/doc/examples/with_test_data.mdwn
index 2808808..1dfa0dc 100644
--- a/doc/examples/with_test_data.mdwn
+++ b/doc/examples/with_test_data.mdwn
@@ -36,7 +36,7 @@ BWA, and produces output like the following.
[bsw2_aln] read 2000 sequences/pairs (843395 bp)...
[samopen] SAM header is present: 167 sequences.
[main] Version: 0.6.2-r126
- [main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V/index A.fastq
+ [main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V-C/index A.fastq
[main] Real time: 1.099 sec; CPU: 8.225 sec
This indicates that 2,000 reads have been processed, representing 843,395 base
diff --git a/html_doc/clonotypeR.html b/html_doc/clonotypeR.html
index aab33f8..3b262f0 100644
--- a/html_doc/clonotypeR.html
+++ b/html_doc/clonotypeR.html
@@ -392,7 +392,7 @@ BWA, and produces output like the following.</p>
<pre><code>[bsw2_aln] read 2000 sequences/pairs (843395 bp)...
[samopen] SAM header is present: 167 sequences.
[main] Version: 0.6.2-r126
-[main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V/index A.fastq
+[main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V-C/index A.fastq
[main] Real time: 1.099 sec; CPU: 8.225 sec
</code></pre>
diff --git a/references/Makefile b/references/Makefile
index de53e5f..e775f3c 100644
--- a/references/Makefile
+++ b/references/Makefile
@@ -4,9 +4,9 @@ gb2fa: TRA@.gb TRB@.gb TRG@.gb
../scripts/gb2fa.bash
bwa-index: V-C.fa
- ln -s ../V-C.fa V/index
- bwa index V/index
- rm V/index
+ ln -s ../V-C.fa V-C/index
+ bwa index V-C/index
+ rm V-C/index
degap: V-C.fa V_after_C.fa J_before_FGxG.fa J-FGxG.fa
for FA in V-C.fa V_after_C.fa J_before_FGxG.fa J-FGxG.fa ; do \
@@ -17,4 +17,4 @@ refresh-data:
R CMD BATCH --no-save J_before_FGxG.R
clean:
- @rm --force --verbose V/index.* V_after_C.Rout J_before_FGxG.Rout
+ @rm --force --verbose V-C/index.* V_after_C.Rout J_before_FGxG.Rout
diff --git a/references/V-C/index.amb b/references/V-C/index.amb
new file mode 100644
index 0000000..353dee2
--- /dev/null
+++ b/references/V-C/index.amb
@@ -0,0 +1 @@
+55126 169 0
diff --git a/references/V-C/index.ann b/references/V-C/index.ann
new file mode 100644
index 0000000..1d5538b
--- /dev/null
+++ b/references/V-C/index.ann
@@ -0,0 +1,339 @@
+55126 169 11
+0 TRAV1 (null)
+0 321 0
+0 TRAV2 (null)
+321 315 0
+0 TRAV3-1 (null)
+636 407 0
+0 TRAV4-1 (null)
+1043 317 0
+0 TRAV5-1 (null)
+1360 333 0
+0 TRAV6-1 (null)
+1693 327 0
+0 TRAV7-1 (null)
+2020 326 0
+0 TRAV6-2 (null)
+2346 330 0
+0 TRAV7D-2 (null)
+2676 327 0
+0 TRAV4D-2 (null)
+3003 321 0
+0 TRAV6D-3 (null)
+3324 327 0
+0 TRAV7D-3 (null)
+3651 327 0
+0 TRAV6D-4 (null)
+3978 329 0
+0 TRAV7D-4 (null)
+4307 327 0
+0 TRAV8D-1 (null)
+4634 327 0
+0 TRAV9D-1 (null)
+4961 327 0
+0 TRAV6D-5 (null)
+5288 327 0
+0 TRAV10D (null)
+5615 322 0
+0 TRAV6D-6 (null)
+5937 337 0
+0 TRAV13D-1 (null)
+6274 313 0
+0 TRAV15D-1/DV6D-1 (null)
+6587 336 0
+0 TRAV3D-2 (null)
+6923 328 0
+0 TRAV9D-2 (null)
+7251 330 0
+0 TRAV4D-3 (null)
+7581 318 0
+0 TRAV5D-2 (null)
+7899 281 0
+0 TRAV12D-2 (null)
+8180 327 0
+0 TRAV9D-3 (null)
+8507 330 0
+0 TRAV5D-3 (null)
+8837 212 0
+0 TRAV12D-3 (null)
+9049 331 0
+0 TRAV15D-2/DV6-2 (null)
+9380 326 0
+0 TRAV9D-4 (null)
+9706 220 0
+0 TRAV4D-4 (null)
+9926 319 0
+0 TRAV5D-4 (null)
+10245 337 0
+0 TRAV6D-7 (null)
+10582 324 0
+0 TRAV7D-6 (null)
+10906 324 0
+0 TRAV13D-3 (null)
+11230 327 0
+0 TRAV8D-2 (null)
+11557 327 0
+0 TRAV16D/DV11 (null)
+11884 312 0
+0 TRAV13D-4 (null)
+12196 327 0
+0 TRAV14D-3/DV8 (null)
+12523 351 0
+0 TRAV15D-3 (null)
+12874 218 0
+0 TRAV7N-4 (null)
+13092 326 0
+0 TRAV9N-1 (null)
+13418 321 0
+0 TRAV6N-5 (null)
+13739 325 0
+0 TRAV10N (null)
+14064 322 0
+0 TRAV6N-6 (null)
+14386 330 0
+0 TRAV11N (null)
+14716 333 0
+0 TRAV7N-5 (null)
+15049 319 0
+0 TRAV12N-1 (null)
+15368 330 0
+0 TRAV13N-1 (null)
+15698 321 0
+0 TRAV14N-1 (null)
+16019 354 0
+0 TRAV15N-1 (null)
+16373 336 0
+0 TRAV3N-2 (null)
+16709 324 0
+0 TRAV9N-2 (null)
+17033 330 0
+0 TRAV4N-3 (null)
+17363 321 0
+0 TRAV5N-2 (null)
+17684 277 0
+0 TRAV12N-2 (null)
+17961 333 0
+0 TRAV9N-3 (null)
+18294 330 0
+0 TRAV5N-3 (null)
+18624 270 0
+0 TRAV12N-3 (null)
+18894 336 0
+0 TRAV13N-2 (null)
+19230 321 0
+0 TRAV14N-2 (null)
+19551 354 0
+0 TRAV15N-2 (null)
+19905 336 0
+0 TRAV3N-3 (null)
+20241 333 0
+0 TRAV9N-4 (null)
+20574 330 0
+0 TRAV4N-4 (null)
+20904 321 0
+0 TRAV5N-4 (null)
+21225 337 0
+0 TRAV6N-7 (null)
+21562 357 0
+0 TRAV7N-6 (null)
(Diff truncated)
</pre>
</div>
change to scripts/VJsplit on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5a4d3c1011b810ff920bfe8bc9fe46d90432a426/
plessy
2014-09-25T07:51:17Z
2014-09-25T07:51:17Z
<div id="change-5a4d3c1011b810ff920bfe8bc9fe46d90432a426" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=scripts/VJsplit;h=4b23919902c58e233c0b8fd2548036581cb027ad;hp=d1433f567ebb282cf611cbe44ddf3ad89d5b723e;hb=5a4d3c1011b810ff920bfe8bc9fe46d90432a426;hpb=2fdcadd0b912d8d31c5fd95b1d04e30013a05dc2" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=scripts%2FVJsplit&do=goto" rel="nofollow">scripts/VJsplit</a>
</span>
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<span class="committer">
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</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-09-25T07:51:17Z" class="relativedate" title="Thu, 25 Sep 2014 07:51:17 +0000">07:51:17 09/25/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Replace slashes by wildcards in EMBOSS USA passed to seqret.<br />
EMBOSS 6.6.6 converts slashes to underscores on the fly. Not sure for<br />
earlier versions.<br />
For example TRAV14D-3/DV8 is converted to TRAV14D-3_DV8, but them<br />
match TRAV14D-3?DV8.<br />
</div>
<div class="diff">
<pre>
diff --git a/scripts/VJsplit b/scripts/VJsplit
index d1433f5..4b23919 100755
--- a/scripts/VJsplit
+++ b/scripts/VJsplit
@@ -49,7 +49,7 @@ do
VECTORSTRIP_V_OUTFILE=$LIBRARY.${V_NAME//\//}.vectorstrip
fi
echo -ne "$V_NAME\t" 1>&2
- V_SEQ=$(seqret -filter $CLONOTYPER_REFERENCE/${V_LIB}-C.fa:$V_NAME[-20:] raw:stdout)
+ V_SEQ=$(seqret -filter $CLONOTYPER_REFERENCE/${V_LIB}-C.fa:${V_NAME//\//?}[-20:] raw:stdout)
# Encode the mapping quality and alignment score in the sequence name
samtools view $EXTRACT_DIR/$LIBRARY.bam $V_NAME |
perl -ne '($score) = /AS:i:(\d+)\t/ ; ($mapq) = (split)[4] ; print "AS_${score}_MQ_${mapq}_$_"' > $LIBRARY-${V_NAME//\//}-filtered.sam
</pre>
</div>
change to vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_ae5e044a195fdc86dd0af7bdfddf27fb37dab0f4/
plessy
2014-09-25T04:33:29Z
2014-09-25T04:33:29Z
<div id="change-ae5e044a195fdc86dd0af7bdfddf27fb37dab0f4" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
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<span class="committer">
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</span>
</div>
<div class="changelog">
Uppercase final letter in 'clonotypeR'.<br />
</div>
<div class="diff">
<pre>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 19da4f5..8679d56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -126,13 +126,13 @@ of the display).
### Detection of V segments
-Run the command `clonotyper detect A.fastq` in the same directory as a copy of
+Run the command `clonotypeR detect A.fastq` in the same directory as a copy of
the file `A.fastq`.
The result is stored in a temporary directory called `extraction_files`, that
will be created if it does not already exist.
-`clonotyper detect` compares the sequences to the reference V segments using
+`clonotypeR detect` compares the sequences to the reference V segments using
BWA, and produces output like the following.
[bsw2_aln] read 2000 sequences/pairs (843395 bp)...
@@ -146,13 +146,13 @@ pairs in total. There were 167 reference V segments, and the version number of
BWA was `0.6.2-r126`. The whole process took less than 10 seconds.
Process the example libraries `B` and `C` similarly with the commands
-`clonotyper detect B.fastq` and `clonotyper detect C.fastq`.
+`clonotypeR detect B.fastq` and `clonotypeR detect C.fastq`.
### Extraction of CDR3 regions
-Run the command `clonotyper extract A` in the same directory as where you ran
-`clonotyper detect A.fastq`. The result is a table stored in a directory
+Run the command `clonotypeR extract A` in the same directory as where you ran
+`clonotypeR detect A.fastq`. The result is a table stored in a directory
called `clonotypes`, that will be created if it does not already exist.
The output is quite voluminous, and indicates which *V* / *J* combinations are
</pre>
</div>
change to vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_0f724d3a35d432366a5b41fc7514af1d89da506a/
plessy
2014-09-25T04:31:40Z
2014-09-25T04:31:40Z
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Corrected a typo.<br />
</div>
<div class="diff">
<pre>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 32f4fe7..19da4f5 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -146,7 +146,7 @@ pairs in total. There were 167 reference V segments, and the version number of
BWA was `0.6.2-r126`. The whole process took less than 10 seconds.
Process the example libraries `B` and `C` similarly with the commands
-`clonotyper detect C.fastq` and `clonotyper detect C.fastq`.
+`clonotyper detect B.fastq` and `clonotyper detect C.fastq`.
### Extraction of CDR3 regions
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_201aadbb8c4442701d1fb987b24f19e5b833d243/
bioc-sync
2014-09-25T04:15:56Z
2014-09-25T04:15:56Z
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 1 commit.<br />
Commit information:<br />
SVN Revision number: 94512<br />
Commit message:<br />
Updated data to test Git-SVN bridge.<br />
Committed by c.plessy<br />
Committed at: 2014-09-25T04:14:48.978745Z<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 8e69f9b..3370138 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
Version: 1.3.1
-Date: 2014-04-08
+Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
Description: High throughput analysis of T cell antigen receptor sequences
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_bd114f490329e5f1a1710ee584823e4329cf0f7b/
c.plessy
2014-09-25T04:14:48Z
2014-09-25T04:14:48Z
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Updated data to test Git-SVN bridge.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@94512 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 8e69f9b..3370138 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
Version: 1.3.1
-Date: 2014-04-08
+Date: 2014-09-25
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
Description: High throughput analysis of T cell antigen receptor sequences
</pre>
</div>
change to vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_e898926ac47d22ea9c3ef33ba96b0947b1c73f25/
c.plessy
2014-09-25T04:13:03Z
2014-09-25T04:13:03Z
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Consists of 2 commits.<br />
Commit information:<br />
Commit id: 51fb79220208de9e7ca472345e524c8b40a3654d<br />
Merge branch 'master' of github.com:charles-plessy/clonotypeR<br />
Committed by: Bioconductor Git-SVN Bridge<br />
Author Name: Bioconductor Git-SVN Bridge<br />
Commit date: 2014-09-24 21:14:00 -0700<br />
Author date: 2014-09-24 21:14:00 -0700<br />
Commit id: ecd472cb2a5a17a4ebe7821a80961252b1b5796b<br />
More spellchecking.<br />
This also tests the Git-SVN bridge.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 13:09:33 +0900<br />
Author date: 2014-09-25 13:09:33 +0900<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@94511 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 3de0e56..32f4fe7 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -57,7 +57,7 @@ library(clonotypeR)
The data is a table of 120 clonotypes in the `extdata` folder of the package.
The command `read_clonotypes` will parse it in a data frame. The clonotypes
-are arbitrarly assigned to three libraries called `A`, `B`, and `C`. The
+are arbitrarily assigned to three libraries called `A`, `B`, and `C`. The
`read_clonotypes` comments determines at load time if the peptidic sequence has
a stop codon or is frame-shifted, and records the information in the
`unproductive` column.
@@ -78,7 +78,7 @@ head(clonotype_table(levels(clonotypes$lib), "J", data=clonotypes))
```
ClonotypeR provides other functions for further analysis. `yassai_identifier`
-calculates a unique indentifier using the `V`, `J`, peptidic and nucleotidic
+calculates a unique identifier using the `V`, `J`, peptidic and nucleotidic
information, following the work of [Yassai et al](http://dx.doi.org/10.1007/s00251-009-0383-x).
```{r yassai_identifier}
@@ -100,7 +100,7 @@ common_clonotypes(data=clonotypes)
```
With deeper data, a typical follow-up would be to identify differentially
-represnted clonotypes between libraries, for instance with the `edgeR` package,
+represented clonotypes between libraries, for instance with the `edgeR` package,
or to calculate distance between libraries, for instance with the
`vegan` package.
@@ -109,7 +109,7 @@ Example data (3 x 2,000 reads)
------------------------------
The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
+is a sub-sample of three sequence libraries of mouse T cell receptors &alpha; (2,000
reads each) made on the 454 Titanium or the 454 junior platforms. The original
libraries will be deposited in public databanks after publication in a
peer-reviewed journal.
@@ -210,7 +210,7 @@ The command `summary(clonotypes)` already provides useful information.
summary(clonotypes)
```
-Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarly named `abc`.
+Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarily named `abc`.
```{r explore_data2}
abc <- clonotype_table(c('A','B','C'), data=clonotypes)
</pre>
</div>
change to Bugs Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier. Bugs/Different_clonotypes_give_the_same_Yassai_identifier. Bugs/Does_not_work_with_EMBOSS_6.6.0. Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_ Bugs/Use_basename_case-insensitively Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file. Bugs/done Bugs/yassai.nomenclature_returns_incorrect_values. Makefile on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_b7802e5dc71d09d8f46e78621cec0e71f3292502/
c.plessy
2014-09-25T04:11:58Z
2014-09-25T04:11:58Z
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Makefile;h=0000000000000000000000000000000000000000;hp=a648f3de8172a0e0d7074cb8f3c729f7861871b9;hb=b7802e5dc71d09d8f46e78621cec0e71f3292502;hpb=74e68018a3bdf448e7cce7d6ec41ff21a45ad99d" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=Makefile" rel="nofollow">Makefile</a>
...
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Revert merge with the branch containing the wiki and the bash scripts.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@94510 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs.mdwn b/Bugs.mdwn
deleted file mode 100644
index 1106591..0000000
--- a/Bugs.mdwn
+++ /dev/null
@@ -1,12 +0,0 @@
-If you've found a bug in clonotypeR, post about it here. [[TODO]] items go
-elsewhere. Link items to [[Bugs/done]] when done.
-
-The [[!shortcut name=commit url="http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s"]].
-You can use it to link to the commit that fixed the bug, as in `\[[!commit 7cf11805d84ff8dc6a537c17e73efa275077915d]]`.
-
-There are [[!pagecount pages="Bugs/* and !Bugs/done and !Bugs/discussion and
-!link(patch) and !link(Bugs/done) and !Bugs/*/*"]] "open" bugs:
-
-[[!inline pages="Bugs/* and !Bugs/done and !Bugs/discussion and
-!link(patch) and !link(Bugs/done) and !Bugs/*/*"
-actions=yes rootpage="Bugs" postformtext="Add a new bug titled:" show=0]]
diff --git a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
deleted file mode 100644
index 7cdfc91..0000000
--- a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
+++ /dev/null
@@ -1,55 +0,0 @@
-Problem
--------
-
-<pre>
-yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
-# takes ages
-
-yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAGCAACCGCAACTTCAAGTGGCCAGAAGCTGGTT", pep="AATATSSGQKLV"))
-## [1] "aTa.2A14N3A16L12"
-# returns immediately.
-</pre>
-
-
-Troubleshooting
----------------
-
-The problematic clonotype comes from read `GWYEMNS10GHZUF`.
-
-<pre>
-&#64;GWYEMNS10GHZUF
-gactAACTGGTACACAGCAGGTTCTGGGTTCTGGATGTGCAGGTACACCTTTAATATGGTCCCCTGGCCAAAAACCAGCTTCTGGCCACTTGAAGTTGCACAGAAGTAGGTGGCTGAGTCTCCAGGCTGAGAGTCTTTGATGTGCAAGGAGAGATTTTTCTCCCTTTTATTGAAGAAGATTGTGAATCGTCCATCTTCCTTTTTATCGGACACTGAACGTATGGCTATCAGGAGAGCAGGGCCTTCCCCAGGGAACTGCTGGTACCATGGGAAGTAGTCAAAAGCACTGTTCTCAtaactagcagttcagaattgcggtctctccttccccagactgtcagagattggagtcgtgggagacaaggcacacaggggataggngngnnnnnnnnnnnnn
-+
-FFF::;;FFFFFFFFIIIIHFFFHF666=&lt;FFGGDDDFFHFDIIIIIIIHHHIIIHFFFD54449662200001335&gt;&gt;AAABDFDDDFDDDFFFFFFFFFFFFFFFFFCCCCCFFFFFFFFFFFFDDBBBBB==110?&#64;&#64;&#64;&#64;&#64;&gt;4455BBA??3357;F4:::;;==D88?AA&lt;;:==BAAAA==??AAB&#64;AAA=&gt;&gt;&gt;222//02A8898BDDFFFDDFFFFFF666:DBAAAABB:::???DD;;;;D?????DDBA?&lt;&lt;&lt;&gt;&lt;&lt;&lt;&lt;000444&lt;8993222233393...:663322&lt;9233776899:;;963326755551111,,,,3313335333799.....23322666726;;;66772222,,,,47400!,!,!!!!!!!!!!!!!
-</pre>
-
-Here is the alignment made by clonotypeR
-
-<pre>
-GWYEMNS10GHZUF 16 TRAV14N-3 105 17 49S17M1I29M1I201M99S * 0 0 NNNNNNNNNNNNNCNCNCCTATCCCCTGTGTGCCTTGTCTCCCACGACTCCAATCTCTGACAGTCTGGGGAAGGAGAGACCGCAATTCTGAACTGCTAGTTATGAGAACAGTGCTTTTGACTACTTCCCATGGTACCAGCAGTTCCCTGGGGAAGGCCCTGCTCTCCTGATAGCCATACGTTCAGTGTCCGATAAAAAGGAAGATGGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAATCTCTCCTTGCACATCAAAGACTCTCAGCCTGGAGACTCAGCCACCTACTTCTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATATTAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTAGTC !!!!!!!!!!!!!,!,!00474,,,,22227766;;;62766622332.....9973335333133,,,,111155557623369;;:9986773329&lt;223366:...3933322223998&lt;444000&lt;&lt;&lt;&lt;&gt;&lt;&lt;&lt;?ABDD?????D;;;;DD???:::BBAAAABD:666FFFFFFDDFFFDDB8988A20//222&gt;&gt;&gt;=AAA&#64;BAA??==AAAAB==:;&lt;AA?88D==;;:::4F;7533??ABB5544&gt;&#64;&#64;&#64;&#64;&#64;?011==BBBBBDDFFFFFFFFFFFFCCCCCFFFFFFFFFFFFFFFFFDDDFDDDFDBAAA&gt;&gt;53310000226694445DFFFHIIIHHHIIIIIIIDFHFFDDDGGFF&lt;=666FHFFFHIIIIFFFFFFFF;;::FFF AS:i:233 XS:i:218 XF:i:3 XE:i:4 XN:i:0
-</pre>
-
-The problem was that the V segment was completely digested in favor of the J segment.
-
-<pre>
- 351 400
-GWYEMNS10GHZUF CTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
-TRAJ16 ~~~~GCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
-TRAV14N-3 CTGTGCAGC...AAGTG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- 401 450
-GWYEMNS10GHZUF TAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTA
-TRAJ16 TAAAGGTGTACCTGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-TRAV14N-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-</pre>
-
-This triggered an infinite loop when calling `is.germline()`.
-
-[[Done]] in `42ab98729c5c77462b5929b00ee973074ae4c1c7`.
-
-Now the function should return as in the following example.
-
-<pre>
-yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
-## [1] "a.A14N3A16L9"
-</pre>
diff --git a/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn b/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
deleted file mode 100644
index a4efb15..0000000
--- a/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
+++ /dev/null
@@ -1,31 +0,0 @@
-Is it a bug in the software or a bug in the concept ?
-
-<pre>
-> rownames(dd)[grep('aAn.1A14-1A43L9', dd.yassai)]
-[1] "TRAV14-1 TRAJ43 GCAGCAGCTAACAACAATGCCCCACGA AAANNNAPR"
-[2] "TRAV14-1 TRAJ43 GCAGCTAATAACAACAATGCCCCACGA AANNNNAPR"
-> V_after_C['TRAV14-1',]
-[1] "GCAGCAAGTG"
-> J_before_FGxG['TRAJ43',]
-[1] "GCAATAACAACAATGCCCCACGA"
-</pre>
-
-<pre>
-aAn.1A14-1A43L9
- A A A N N N A P R
-GCA GCA GCT AAC AAC AAT GCC CCA CGA
-GCA GCA agt g
- gc aaT AAC AAC AAT GCC CCA CGA
-</pre>
-
-<pre>
-aAn.1A14-1A43L9
- A A N N N N A P R
-GCA GCT AAT AAC AAC AAT GCC CCA CGA
-GCA GCa agt g
- gc AAT AAC AAC AAT GCC CCA CGA
-</pre>
-
-----
-
-This is a collision (different colonotypes giving the same Yassai ID) rather than a bug in the implementation → [[done]].
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
deleted file mode 100644
index c95cbe8..0000000
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ /dev/null
@@ -1,18 +0,0 @@
-The reason is the following bug in EMBOSS.
-
-<pre>
-echo -e '>A\nAAAAAA' > test-1.fa
-cat test-1.fa
-# >A
-# AAAAAA
-seqret test-1.fa:A stdout
-# Read and write (return) sequences
-# >A
-# AAAAAA
-mkdir test
-seqret test-1.fa:A stdout
-# Read and write (return) sequences
-# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
-# Error: Unable to read sequence 'test-1.fa:A'
-# Died: seqret terminated: Bad value for '-sequence' and no prompt
-</pre>
diff --git a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
deleted file mode 100644
index 1648dce..0000000
--- a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
+++ /dev/null
@@ -1,13 +0,0 @@
-<pre>
-> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
-[1] "tg.integer(0)A2A61L13"
-</pre>
-
-[[Done]] in `2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd`, by return an empty chain instead of `integer(0)` when receiving an empty chain.
-
-Result after correction:
-
-<pre>
-> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
-[1] "tg.A2A61L13"
-</pre>
diff --git a/Bugs/Use_basename_case-insensitively.mdwn b/Bugs/Use_basename_case-insensitively.mdwn
deleted file mode 100644
index 95a3173..0000000
--- a/Bugs/Use_basename_case-insensitively.mdwn
+++ /dev/null
@@ -1,6 +0,0 @@
-Problem:
-
- $ basename foo.fastq .fastq
- foo
- $ basename foo.FASTQ .fastq
- foo.FASTQ
diff --git a/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn b/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
deleted file mode 100644
index 3899e4e..0000000
--- a/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
+++ /dev/null
@@ -1,18 +0,0 @@
-This would prevent horrors like:
-
-<pre>
-$ ../scripts/clonotypeR detect .fastq
-[bam_header_read] EOF marker is absent. The input is probably truncated.
-[bsw2_aln] fail to open file '.fastq'. Abort!
-[samopen] SAM header is present: 169 sequences.
-[sam_read1] reference 'SN:TRDV5 LN:344
-3
-
-19
-
-3
-
-
-' is recognized as '*'.
-[main_samview] truncated file.
-</pre>
diff --git a/Bugs/done.mdwn b/Bugs/done.mdwn
deleted file mode 100644
index 0a666ab..0000000
--- a/Bugs/done.mdwn
+++ /dev/null
(Diff truncated)
</pre>
</div>
change to vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_ecd472cb2a5a17a4ebe7821a80961252b1b5796b/
plessy
2014-09-25T04:09:33Z
2014-09-25T04:09:33Z
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<pre>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 3de0e56..32f4fe7 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -57,7 +57,7 @@ library(clonotypeR)
The data is a table of 120 clonotypes in the `extdata` folder of the package.
The command `read_clonotypes` will parse it in a data frame. The clonotypes
-are arbitrarly assigned to three libraries called `A`, `B`, and `C`. The
+are arbitrarily assigned to three libraries called `A`, `B`, and `C`. The
`read_clonotypes` comments determines at load time if the peptidic sequence has
a stop codon or is frame-shifted, and records the information in the
`unproductive` column.
@@ -78,7 +78,7 @@ head(clonotype_table(levels(clonotypes$lib), "J", data=clonotypes))
```
ClonotypeR provides other functions for further analysis. `yassai_identifier`
-calculates a unique indentifier using the `V`, `J`, peptidic and nucleotidic
+calculates a unique identifier using the `V`, `J`, peptidic and nucleotidic
information, following the work of [Yassai et al](http://dx.doi.org/10.1007/s00251-009-0383-x).
```{r yassai_identifier}
@@ -100,7 +100,7 @@ common_clonotypes(data=clonotypes)
```
With deeper data, a typical follow-up would be to identify differentially
-represnted clonotypes between libraries, for instance with the `edgeR` package,
+represented clonotypes between libraries, for instance with the `edgeR` package,
or to calculate distance between libraries, for instance with the
`vegan` package.
@@ -109,7 +109,7 @@ Example data (3 x 2,000 reads)
------------------------------
The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
+is a sub-sample of three sequence libraries of mouse T cell receptors &alpha; (2,000
reads each) made on the 454 Titanium or the 454 junior platforms. The original
libraries will be deposited in public databanks after publication in a
peer-reviewed journal.
@@ -210,7 +210,7 @@ The command `summary(clonotypes)` already provides useful information.
summary(clonotypes)
```
-Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarly named `abc`.
+Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarily named `abc`.
```{r explore_data2}
abc <- clonotype_table(c('A','B','C'), data=clonotypes)
</pre>
</div>
change to man/common_clonotypes.Rd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_74e68018a3bdf448e7cce7d6ec41ff21a45ad99d/
c.plessy
2014-09-25T04:03:52Z
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Consists of 2 commits.<br />
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Commit id: 4e7034c69e443882fca6fe517088d3ac3658a6d0<br />
Merge branch 'master' of github.com:charles-plessy/clonotypeR<br />
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Checked spelling.<br />
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Author Name: Charles Plessy<br />
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<pre>
diff --git a/man/common_clonotypes.Rd b/man/common_clonotypes.Rd
index 3d239ca..9005ee0 100644
--- a/man/common_clonotypes.Rd
+++ b/man/common_clonotypes.Rd
@@ -29,7 +29,7 @@ quantitatively the overlap between each pair of libraries.
\arguments{
\item{group1}{A character vector containing clonotype library names.}
\item{group2}{A character vector containing clonotype library names.}
- \item{mode}{Only when producing a matrix of pairwise comparisions: \dQuote{count} (default) or \dQuote{abundance}, see below.}
+ \item{mode}{Only when producing a matrix of pairwise comparisons: \dQuote{count} (default) or \dQuote{abundance}, see below.}
\item{data}{A clonotype table where the data is stored.}
}
</pre>
</div>
change to man/common_clonotypes.Rd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_5ed6cd02c7cd5701860ff1d20e80f509aa64bd96/
plessy
2014-09-25T04:03:28Z
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diff --git a/man/common_clonotypes.Rd b/man/common_clonotypes.Rd
index 3d239ca..9005ee0 100644
--- a/man/common_clonotypes.Rd
+++ b/man/common_clonotypes.Rd
@@ -29,7 +29,7 @@ quantitatively the overlap between each pair of libraries.
\arguments{
\item{group1}{A character vector containing clonotype library names.}
\item{group2}{A character vector containing clonotype library names.}
- \item{mode}{Only when producing a matrix of pairwise comparisions: \dQuote{count} (default) or \dQuote{abundance}, see below.}
+ \item{mode}{Only when producing a matrix of pairwise comparisons: \dQuote{count} (default) or \dQuote{abundance}, see below.}
\item{data}{A clonotype table where the data is stored.}
}
</pre>
</div>
change to DESCRIPTION NAMESPACE on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_a36f40eaa87548985dc0e4d440fa43701268329e/
c.plessy
2014-09-25T03:28:04Z
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 2 commits.<br />
Commit information:<br />
Commit id: c32c335cc2b3817a74e1129d81d775dfd6a19f61<br />
Merge branch 'master' of github.com:charles-plessy/clonotypeR<br />
Committed by: Bioconductor Git-SVN Bridge<br />
Author Name: Bioconductor Git-SVN Bridge<br />
Commit date: 2014-09-24 20:29:00 -0700<br />
Author date: 2014-09-24 20:29:00 -0700<br />
Commit id: e2388f68d34bcb0b1d72475237341782eed2479c<br />
Explicitely import setMethod in NAMESPACE.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 11:27:33 +0900<br />
Author date: 2014-09-25 11:27:33 +0900<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@94507 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index c73ec16..8e69f9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: High throughput analysis of T cell antigen receptor sequences
The purpose of this package is to process and quantitatively analyse millions
of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
License: file LICENSE
-Depends: methods
+Imports: methods
Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
VignetteBuilder: knitr
Packaged: 2013-12-11 10:22:39 UTC; charles
diff --git a/NAMESPACE b/NAMESPACE
index d75f824..2d083c2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,2 @@
+importFrom(methods, setMethod)
exportPattern("^[[:alpha:]]+")
</pre>
</div>
change to Bugs Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier. Bugs/Different_clonotypes_give_the_same_Yassai_identifier. Bugs/Does_not_work_with_EMBOSS_6.6.0. Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_ Bugs/Use_basename_case-insensitively Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file. Bugs/done Bugs/yassai.nomenclature_returns_incorrect_values. Makefile on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_319bc5bcca445b03c65c9b304e52c780097916ab/
c.plessy
2014-09-25T02:29:44Z
2014-09-25T02:29:44Z
<div id="change-319bc5bcca445b03c65c9b304e52c780097916ab" class="metadata">
<span class="desc"><br />Changed pages:</span>
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Makefile;h=a648f3de8172a0e0d7074cb8f3c729f7861871b9;hp=0000000000000000000000000000000000000000;hb=319bc5bcca445b03c65c9b304e52c780097916ab;hpb=431538c61f3167a3e9b78565bc744eba0258ed81" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=Makefile" rel="nofollow">Makefile</a>
...
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<span class="changedate"><time datetime="2014-09-25T02:29:44Z" class="relativedate" title="Thu, 25 Sep 2014 02:29:44 +0000">02:29:44 09/25/14</time></span>
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 380 commits.<br />
Commit information:<br />
Commit id: de449193bde6e56a204d3b12c7f4e489a780e4b2<br />
Merge branch 'bioc'<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-09-25 11:00:49 +0900<br />
Author date: 2014-09-25 11:00:49 +0900<br />
Commit id: 0838bc06272e87c0690f093a017cde8a9cc10313<br />
News entry for the new stable release.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-06-05 19:40:12 +0900<br />
Author date: 2014-06-05 19:40:12 +0900<br />
Commit id: 67aa2eac309df5bf8d5dbc790661db102145d692<br />
Does not work with EMBOS 6.6.0.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2014-06-05 05:22:35 +0000<br />
Author date: 2014-06-05 05:22:35 +0000<br />
Commit id: fe4ae4f131d3c5fc8d5aebd5873d7de109c1b0b7<br />
Should use `basename` canse-insensitively…<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2014-06-04 22:38:29 +0000<br />
Author date: 2014-06-04 22:38:29 +0000<br />
Commit id: 517e35af4a8ad194bed6ea3d187c73e5b97490b7<br />
Merge branch 'bioc'<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-09 12:45:46 +0900<br />
Author date: 2014-04-09 12:45:46 +0900<br />
Commit id: 23598ee1b592a99be9cf58602b0f214c2980453a<br />
Merge branch 'bioc'<br />
Conflicts:<br />
DESCRIPTION<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-08 15:45:15 +0900<br />
Author date: 2014-04-08 15:45:15 +0900<br />
Commit id: d404d2c8f9b682404b64d2d5e8deb29954edc499<br />
Merge branch 'bioc'<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-03 14:03:24 +0900<br />
Author date: 2014-04-03 14:03:24 +0900<br />
Commit id: bd21f9c77e7083e183d22287c4f79e8c6161d62e<br />
Documentation updates.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-03 14:02:11 +0900<br />
Author date: 2014-04-03 14:02:11 +0900<br />
Commit id: 8a633d4908bd1176d9dced6ba47acfc469aa7a3f<br />
Merge branch 'bioc'<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-03 13:49:30 +0900<br />
Author date: 2014-04-03 13:49:30 +0900<br />
Commit id: bb7e511573b44b0ecd95e5d643dceb6adcc103a2<br />
Merge branch 'bioc'<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-03 13:19:06 +0900<br />
Author date: 2014-04-03 13:19:06 +0900<br />
Commit id: de328b9f0a5035662eb934d79dd876ae72a1ba0b<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-03 11:28:17 +0900<br />
Author date: 2014-04-03 11:28:17 +0900<br />
Commit id: d16322c96db5046f113bfa982e8a621444324ab5<br />
Merge branch 'bioc'<br />
Conflicts:<br />
DESCRIPTION<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2014-04-03 11:27:03 +0900<br />
Author date: 2014-04-03 11:27:03 +0900<br />
Commit id: 2767b62c7c87359ca87daaf28e4ec5dec44a5b6f<br />
No full source archive available for the moment.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-19 16:21:39 +0000<br />
Author date: 2013-12-19 16:21:39 +0000<br />
Commit id: 56784b6503a5de8205789f19a23bbf40cf9750ea<br />
Commited 1.1.3 to Bioconductor.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 19:27:09 +0900<br />
Author date: 2013-12-11 19:27:09 +0900<br />
Commit id: d2488356f56b6c332a4796d2d3f0245bfcc5e558<br />
Indicate the position of the V-J junction when there is no codon ID to indicate.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 19:19:01 +0900<br />
Author date: 2013-12-11 19:19:01 +0900<br />
Commit id: ef4a8fe53efae1baa5df16677edbac30911463ff<br />
Flag and exclude ambiguous DNA sequences.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 17:59:27 +0900<br />
Author date: 2013-12-11 17:59:27 +0900<br />
Commit id: fe95743d1153f6288c987a796ad710b6fba2f1c6<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 14:31:03 +0900<br />
Author date: 2013-12-11 14:31:03 +0900<br />
Commit id: 08727c97529f33931c5d13aeff3e16dc39c29ab7<br />
Problem solved by better checking the input.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-11 05:29:37 +0000<br />
Author date: 2013-12-11 05:29:37 +0000<br />
Commit id: e4d102a595c15459574a5a175124aac69ac9952b<br />
Added example.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-11 05:26:15 +0000<br />
Author date: 2013-12-11 05:26:15 +0000<br />
Commit id: 2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd<br />
Return empty chain instead of integer(0) when receiving an empty chain.<br />
Closes: Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 14:26:05 +0900<br />
Author date: 2013-12-11 14:26:05 +0900<br />
Commit id: cb56f5611fc8532cac80bf527b1d9e8d8524586e<br />
Broke the infinite loop.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-11 05:23:48 +0000<br />
Author date: 2013-12-11 05:23:48 +0000<br />
Commit id: bc0c6046cdfbb32a74a0741548015e01f0c5f659<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 14:21:45 +0900<br />
Author date: 2013-12-11 14:21:45 +0900<br />
Commit id: 42ab98729c5c77462b5929b00ee973074ae4c1c7<br />
Break infinite loop when the whole CDR3 sequence is identical to the germline reference.<br />
Closes: Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-11 14:19:17 +0900<br />
Author date: 2013-12-11 13:33:04 +0900<br />
Commit id: e6f8d079888dc3dcffe677ef1a042313fc03c817<br />
Alignment to the J region is correct as well.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-05 08:23:41 +0000<br />
Author date: 2013-12-05 08:23:41 +0000<br />
Commit id: da4a4c5f6c41041d48fda34cb05ce8ba908cd47c<br />
Alignment of the V region is correct.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-05 08:22:03 +0000<br />
Author date: 2013-12-05 08:22:03 +0000<br />
Commit id: 51e8e91ca69d36b2ec625de2b61c6c21d3663819<br />
Escaped using the Highlight command<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-05 07:59:07 +0000<br />
Author date: 2013-12-05 07:59:07 +0000<br />
Commit id: eb7eaedbf22419eaa200afd8dd97d4ff7c1f782f<br />
Alignment in SAM format.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-05 07:46:39 +0000<br />
Author date: 2013-12-05 07:46:39 +0000<br />
Commit id: a3b445a51fe755d691cf87b9533933d50c71ee94<br />
Found the problematic read.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-05 07:44:59 +0000<br />
Author date: 2013-12-05 07:44:59 +0000<br />
Commit id: 47bba4876cbe49b3a6415bbb4f6f6a6a3007ce41<br />
Found a clonotype that makes yassai_identifier() very slow.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-12-05 05:41:02 +0000<br />
Author date: 2013-12-05 05:41:02 +0000<br />
Commit id: 261d18f4a8f6a042c2d9602e352df47412bad27d<br />
Refreshed documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-05 13:21:34 +0900<br />
Author date: 2013-12-05 13:21:34 +0900<br />
Commit id: 8b85bb373c930b6f1ef506b3ade2bbbc569d3775<br />
New "long" option to yassai_identifier(), to avoid collisions.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-05 13:21:12 +0900<br />
Author date: 2013-12-05 13:21:12 +0900<br />
Commit id: 00f4895d4a172de8fd3109125fc1435e6b2d06a2<br />
Cosmetic reorganisations.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-05 11:34:27 +0900<br />
Author date: 2013-12-05 11:34:27 +0900<br />
Commit id: 0ff5028ed5f320f1e5c75d4657f0bcee6c9c49dd<br />
Simplification and standardisation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-12-05 11:22:40 +0900<br />
Author date: 2013-12-05 11:22:40 +0900<br />
Commit id: 2232d06fa83e353a95cc31851b904d19de8711d6<br />
Another software for analysing TCRs.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-11-20 00:56:00 +0000<br />
Author date: 2013-11-20 00:56:00 +0000<br />
Commit id: 95b2833ad6e5882f1d3f34615830512b51db1da4<br />
Actually, in this collision the translations are different.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-11-20 00:49:14 +0000<br />
Author date: 2013-11-20 00:49:14 +0000<br />
Commit id: baed72501169ddf3ff3d891131f2dfc73a366aec<br />
Corrected aminoacid sequence. Finally, this is a collision.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-11-20 00:44:39 +0000<br />
Author date: 2013-11-20 00:44:39 +0000<br />
Commit id: c32e4a3cc8444cd5e593f1c31a7e359112fbd827<br />
Latest versions on NCBI, updating TRDV5.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-11-19 20:33:32 +0900<br />
Author date: 2013-11-19 19:47:15 +0900<br />
Commit id: f4d3784867dfea3890eaed4612f99fd847c77915<br />
Corrected a typo.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2013-11-19 10:32:20 +0000<br />
Author date: 2013-11-19 10:32:20 +0000<br />
Commit id: 3ca955591dfc25fc68d092b4943ed216ca8e821d<br />
Not a bug.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-11-19 00:42:05 +0000<br />
Author date: 2013-11-19 00:42:05 +0000<br />
Commit id: 08d60b3329e96780e6ec1d339302b088f6ca7f60<br />
Split by codons.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-11-19 00:34:29 +0000<br />
Author date: 2013-11-19 00:34:29 +0000<br />
Commit id: b60fca260bd7b9a65982123de01c7c42b1ba3daa<br />
Different clonotypes give same ID ?<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2013-11-19 00:29:48 +0000<br />
Author date: 2013-11-19 00:29:48 +0000<br />
Commit id: d9b8de3e75728ad5b1d2a2155bd433843f4f1c8f<br />
Bug in yassai_identifier()<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2013-11-18 10:42:49 +0000<br />
Author date: 2013-11-18 10:42:49 +0000<br />
Commit id: 606a691a190592d7cff6038811ebe0b1f04f0049<br />
Corrected a typo.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-31 18:12:47 +0900<br />
Author date: 2013-10-31 18:12:47 +0900<br />
Commit id: 1784e2b9312999da0a70da26df0cadd0880494fc<br />
clonotype_table: new option to randomly "sample" libraries.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-23 19:57:59 +0900<br />
Author date: 2013-10-23 19:57:59 +0900<br />
Commit id: 9ff7927026d58cd082f284097fec448118640f6b<br />
No default table anymore.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-23 18:01:25 +0900<br />
Author date: 2013-10-23 18:01:25 +0900<br />
Commit id: 36f5e57c35b86a59329a33028b5cf8250af84def<br />
Corrected minor formatting error in the documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-23 17:08:50 +0900<br />
Author date: 2013-10-23 17:08:50 +0900<br />
Commit id: 1702447155fa521184444ec18f7b3c54cbe27b38<br />
Refreshed HTML documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-17 19:00:24 +0900<br />
Author date: 2013-10-17 19:00:24 +0900<br />
Commit id: 04608179a93c4f6710e92b8f48b8afe1070bf5c8<br />
common_clonotypes: new mode to calculate the "abundance" relatively to one library.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-17 19:00:03 +0900<br />
Author date: 2013-10-17 18:50:10 +0900<br />
Commit id: 6df141e961f24c6c5cbfd4a0a13ca3eac7274b19<br />
Double the speed, taking advantage of the symmetry.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-17 15:55:45 +0900<br />
Author date: 2013-10-17 15:55:45 +0900<br />
Commit id: 13e106a7bcf2bac307b74dbe37c347e391c76db0<br />
Made common_clonotypes a S4 function.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-17 15:50:56 +0900<br />
Author date: 2013-10-17 15:50:56 +0900<br />
Commit id: 6db01d0bbb9476e645977090a7b0bec8e245ef9e<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-16 16:21:15 +0900<br />
Author date: 2013-10-16 16:21:15 +0900<br />
Commit id: a7f701ba0e21c8a801115c90c7d50b4f11f72f7c<br />
New development branch.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-16 15:52:17 +0900<br />
Author date: 2013-10-16 15:52:17 +0900<br />
Commit id: 5ea2135a5e302b8adafcf7edb8012b6a471051d1<br />
Point to the stable version of Bioconductor.<br />
Committed by: admin<br />
Author Name: https://plessy-riken-jp.myopenid.com/<br />
Commit date: 2013-10-15 22:47:14 +0000<br />
Author date: 2013-10-15 22:47:14 +0000<br />
Commit id: 877d38c95c8e21f41747030426b4844f1600e945<br />
Point to the stable version of Bioconductor.<br />
Committed by: admin<br />
Author Name: https://plessy-riken-jp.myopenid.com/<br />
Commit date: 2013-10-15 22:46:35 +0000<br />
Author date: 2013-10-15 22:46:35 +0000<br />
Commit id: 17952327295bd9a862d9295db23b8dda4ebc9e46<br />
Updating description and releasing 0.99.6.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 20:32:00 +0900<br />
Author date: 2013-10-07 20:31:37 +0900<br />
Commit id: 167637b6e6bbd928a3800d42518cb0ec93d32474<br />
Correct syntax error.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 20:28:49 +0900<br />
Author date: 2013-10-07 20:28:49 +0900<br />
Commit id: 9e2e2de37a8d8aca10e2c07898b38a1059709bbe<br />
Refreshed.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 20:27:26 +0900<br />
Author date: 2013-10-07 20:27:26 +0900<br />
Commit id: b3008e36c563446be4fb08cde93826059da07ce6<br />
Mention Bioconductor on the front page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 20:26:58 +0900<br />
Author date: 2013-10-07 20:26:58 +0900<br />
Commit id: 5796401be556310df17e32e4318d54ef7d7f85c7<br />
Added unit tests for yassai_identifier(), and unbroke it by the way.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 19:55:01 +0900<br />
Author date: 2013-10-07 19:55:01 +0900<br />
Commit id: 1b0ed175787e98c38fea3fd8a5e5d6c8cd408545<br />
Unbreak again the output when there is only one clonotype.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 19:44:50 +0900<br />
Author date: 2013-10-07 19:44:50 +0900<br />
Commit id: 5d9f507c1f2bc79148ce95ec33bc62c3b2a5ca2c<br />
Corrected minor syntax error.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-10-07 19:28:32 +0900<br />
Author date: 2013-10-07 19:28:32 +0900<br />
Commit id: 246b1e3ed20695e559bba51356a2a7cc9ce60c25<br />
The `R` package is also distributed on Bioconductor.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-08-02 13:30:45 +0900<br />
Author date: 2013-08-02 13:30:45 +0900<br />
Commit id: 0d29dcd812655bb18f6da99b83ea457e394895e5<br />
Unified the syntax of common_clonotypes and unique_clonotypes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-08-01 11:22:19 +0900<br />
Author date: 2013-08-01 11:22:19 +0900<br />
Commit id: bff994b1f14ab6665eedc15598df5e83ae8254b0<br />
Resubmitted clonotypeR_0.99.5.tar.gz to Bioconductor.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-05-07 21:28:42 +0900<br />
Author date: 2013-05-07 21:28:42 +0900<br />
Commit id: 215825af72dc8d3369b1e9dad056673ca2fcada1<br />
Add vignette to html_doc; refresh.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-05-07 21:14:47 +0900<br />
Author date: 2013-05-07 21:14:47 +0900<br />
Commit id: fbfe17c884da59b2a3bbab07575971eb588bd12e<br />
Rework vignette to use additional example data.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-05-07 21:08:06 +0900<br />
Author date: 2013-05-07 21:08:06 +0900<br />
Commit id: 6e3d48de97f5df855917fc55ed06ff7f315ee3a1<br />
Clonotypes extracted from example_data.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-05-07 20:51:18 +0900<br />
Author date: 2013-05-07 20:51:18 +0900<br />
Commit id: 8de1988b83f118767b0abfabb988ad769a7dcabf<br />
Corrected a typo.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-05-07 11:41:02 +0000<br />
Author date: 2013-05-07 11:41:02 +0000<br />
Commit id: f1a95ffc338cc9628aa043f8a2319efe33caec09<br />
No time today.<br />
Committed by: admin<br />
Author Name: https://launchpad.net/~plessy<br />
Commit date: 2013-05-07 11:38:20 +0000<br />
Author date: 2013-05-07 11:38:20 +0000<br />
Commit id: 815fbcbae66770f01649bd9c7e65f90569240b4f<br />
Added executable example with test data to the vignette.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-05-01 21:55:33 +0900<br />
Author date: 2013-05-01 21:54:32 +0900<br />
Commit id: 5e658adbd8fb8a2b34511f2f0e9db94335145b0e<br />
Moved vignettes to root for automatic building.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-05-01 21:52:46 +0900<br />
Author date: 2013-05-01 21:52:46 +0900<br />
Commit id: 963544b03c57819095ba459d46ebed561d9762d0<br />
Resubmitted 0.99.3 to Bioconductor.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-26 13:29:56 +0900<br />
Author date: 2013-04-26 13:29:56 +0900<br />
Commit id: 21de5ed25d5afb0bb7e5c9cab6b3105e98a99f52<br />
Refreshed documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-26 13:25:26 +0900<br />
Author date: 2013-04-26 13:25:26 +0900<br />
Commit id: 287c9829612cd1a0407b9d15178ad5548fc50396<br />
Describe the extra data in a common manual page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-26 13:24:15 +0900<br />
Author date: 2013-04-26 13:24:15 +0900<br />
Commit id: b5e5bc8c46e47174722c054b419360a9a256b30a<br />
Correct source code and documentation after moving data to 'inst/extdata'.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-26 12:46:41 +0900<br />
Author date: 2013-04-26 10:40:12 +0900<br />
Commit id: dfe97762cf7c1e827de216bbcbf056bbfeacd4f3<br />
Moved data to 'extdata' as it is not in the '.Rd' format.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-26 10:34:58 +0900<br />
Author date: 2013-04-26 10:34:58 +0900<br />
Commit id: 6e27d1f7f50aa721240da77a763b09e64fe1e8ef<br />
Renamed 'doc' director to 'vignettes' to enable auto-building of the knittr vignette.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-26 10:30:56 +0900<br />
Author date: 2013-04-26 10:30:56 +0900<br />
Commit id: 14f4c3a0fd67591d930df4a550cf9ea25fa8cc53<br />
Refreshed documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-18 09:22:59 +0900<br />
Author date: 2013-04-18 09:22:59 +0900<br />
Commit id: f84db0e8fdcb1a6c03b81c4230c2b8b5c9504a26<br />
0.99.2<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:56:30 +0900<br />
Author date: 2013-04-15 21:56:30 +0900<br />
Commit id: 7cf966e77891afcb2d85aa25600cd07c661df9ec<br />
Declare methods.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:54:25 +0900<br />
Author date: 2013-04-15 21:54:25 +0900<br />
Commit id: 87ab884780b23897a64a17679b23de4271ed65c0<br />
Declare encoding.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:54:14 +0900<br />
Author date: 2013-04-15 21:54:14 +0900<br />
Commit id: 022bebfd23ea34b53cd0c66144481296e0e6832b<br />
Point to license file instead of using unknown keyword (CC0).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:30:48 +0900<br />
Author date: 2013-04-15 21:30:48 +0900<br />
Commit id: c6def55b5a3b83452d39323ef8747de9d065a230<br />
Mention that the V and J data can be changed.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:30:17 +0900<br />
Author date: 2013-04-15 21:30:17 +0900<br />
Commit id: 54772072fccb68a5f775c3d0091c6ce6abff20fa<br />
Mention that the data is from mouse.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:28:43 +0900<br />
Author date: 2013-04-15 21:28:43 +0900<br />
Commit id: 696cb2bc3af330f78f025ffb8092d9f5c2c78427<br />
yassai_identifier: correct multiple output bug when input is a single clonotype.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 21:15:12 +0900<br />
Author date: 2013-04-15 21:15:12 +0900<br />
Commit id: edd71c4cce53992e8adc97afa27acb59c42267df<br />
Call S4 methods only.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 20:33:28 +0900<br />
Author date: 2013-04-15 20:33:28 +0900<br />
Commit id: c0118e3fc2c9f472bab223dd30b31f5fee3e8468<br />
yassai_identifier: load codon_ids as characters.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 20:22:17 +0900<br />
Author date: 2013-04-15 20:22:17 +0900<br />
Commit id: 5bddce379f902d859e3a7667a8386786c91e5e47<br />
Load data from within function; remove un-necessary checks.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 20:01:00 +0900<br />
Author date: 2013-04-15 20:01:00 +0900<br />
Commit id: 7722f3669a425ee6cc78257437479353e7609479<br />
Use a S4 method to facilitate the change or reference sequences.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 19:15:00 +0900<br />
Author date: 2013-04-15 19:15:00 +0900<br />
Commit id: b4aa7dbfadcc4c5179ff513a8acbc37e2c01032a<br />
Replace DOI by PMID.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 16:32:17 +0900<br />
Author date: 2013-04-15 16:32:17 +0900<br />
Commit id: cd259b4799e155c52039a17bf3d0b4cc25ea8f93<br />
Mention Decombinator.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 16:30:25 +0900<br />
Author date: 2013-04-15 16:30:25 +0900<br />
Commit id: 4e780a457c5b8f522a61cea1f4309de109d30c72<br />
Mention that only mouse is supported currently.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 14:43:09 +0900<br />
Author date: 2013-04-15 14:43:09 +0900<br />
Commit id: c7e4dcbd016e84a0b8be69243a054e1655053c91<br />
Correct confusion between human and mouse.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 14:22:16 +0900<br />
Author date: 2013-04-15 14:22:16 +0900<br />
Commit id: e064fc66e7bac6a8c98b59b45e519a660539fca4<br />
Link to RefSeq's TCR loci for Human.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 14:07:41 +0900<br />
Author date: 2013-04-15 14:07:41 +0900<br />
Commit id: a3b6ea1cac7c3fbeb4366f169cde34722c3e0b94<br />
Delete old PDF vignette.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:45:49 +0900<br />
Author date: 2013-04-15 13:45:49 +0900<br />
Commit id: 5781783e0dd3868e503c7ee3d98188607fc843c2<br />
Do not build a PDF vignette.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:45:33 +0900<br />
Author date: 2013-04-15 13:45:33 +0900<br />
Commit id: b9d0aa92434f360b3f23e8eb05c0da65c90d2ea5<br />
Refreshed PDF vignette.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:29:35 +0900<br />
Author date: 2013-04-15 13:29:35 +0900<br />
Commit id: 906aadcd4932fe78b48a539d7aebeb8d33922283<br />
Update date.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:28:45 +0900<br />
Author date: 2013-04-15 13:28:45 +0900<br />
Commit id: 8c423487f471c52a3b6ec21a232ec7d23b097bbb<br />
Adjust whitespace.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:26:51 +0900<br />
Author date: 2013-04-15 13:26:51 +0900<br />
Commit id: d7457f354d8bc9b8e0b945ef8eb289236aafb004<br />
Use knitr::knitr as in the R-exts manual.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:23:40 +0900<br />
Author date: 2013-04-15 13:23:40 +0900<br />
Commit id: 8fe447b31ba96d887d5fbd7c6e48dc7f717505a1<br />
Correct whitespace.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:18:36 +0900<br />
Author date: 2013-04-15 13:18:36 +0900<br />
Commit id: e3671747c8ed17e5365e3b26b26d894fe1541dc6<br />
Minor change of the auto-generated documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:13:27 +0900<br />
Author date: 2013-04-15 13:13:27 +0900<br />
Commit id: 7518dec2320343ae89a82ae05d0ed109eb87d1df<br />
Build vignette with Knitr.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 13:12:08 +0900<br />
Author date: 2013-04-15 13:12:08 +0900<br />
Commit id: 3934ced36d088184ccca45de2871e82b8cbf5589<br />
Vignette inspired from doc/examples/with_test_data.mdwn.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 11:38:05 +0900<br />
Author date: 2013-04-15 11:38:05 +0900<br />
Commit id: d0d8ff9cdea8a21b07a63fcba84b833689bf65d1<br />
Use a syntax similar to the Markdown vignette.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 11:36:45 +0900<br />
Author date: 2013-04-15 11:36:45 +0900<br />
Commit id: 67a7959b669482499a9cac1b06dad42d864cbc05<br />
Removed spurius line.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 11:23:49 +0900<br />
Author date: 2013-04-15 11:23:49 +0900<br />
Commit id: 1490559fb26a4f2e34042177b1bc5e025972bfe2<br />
Build vignette with knitr.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 10:25:44 +0900<br />
Author date: 2013-04-15 10:25:44 +0900<br />
Commit id: ad181fefec0beea6628cae73c8d8ed0b166c0783<br />
Preparing conversion to Markdown format.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-15 10:22:29 +0900<br />
Author date: 2013-04-15 10:22:29 +0900<br />
Commit id: 268c48c41d9fdb654d440134a705e4c1ddf85c78<br />
Update affiliations.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-12 09:29:43 +0900<br />
Author date: 2013-04-12 09:29:43 +0900<br />
Commit id: 5f13c20bcc6616c64a6e17c0c37ce1e7cf8e6ce1<br />
Mention the CLST.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-11 09:55:58 +0900<br />
Author date: 2013-04-11 09:55:58 +0900<br />
Commit id: 6daa7dc64bb4b527677048fa61249238e300ad1b<br />
Mention the OSC as recipient of the MEXT grant.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-08 14:56:02 +0900<br />
Author date: 2013-04-08 14:56:02 +0900<br />
Commit id: 05c8fc7b9777cf498da5d1e9e413e35681ab08f0<br />
Mention acknowledgement and license in README.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-04-08 13:44:56 +0900<br />
Author date: 2013-04-08 13:44:56 +0900<br />
Commit id: c0434a694d7371a69d7665e28c2649f1432bc209<br />
Refreshed HTML documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-27 14:35:05 +0900<br />
Author date: 2013-02-27 14:35:05 +0900<br />
Commit id: c69abf1c31fb192496dfbe2b254e782afea5d8e8<br />
clonotypes.txt.gz: moved from data to inst/extdata.<br />
It has to ble loaded through read_clonotypes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-27 13:58:47 +0900<br />
Author date: 2013-02-27 13:58:47 +0900<br />
Commit id: d81ac599776ecbf97d498537bf064532942d9168<br />
Recompressed the data files.<br />
This makes the source repository similar to the binary package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-27 13:38:14 +0900<br />
Author date: 2013-02-27 13:21:33 +0900<br />
Commit id: 388c8e69dab3642f11cee5349c6a8019819b7a80<br />
yassai_identifier: disambiguate 'head' to 'header'.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-27 11:21:10 +0900<br />
Author date: 2013-02-27 11:21:10 +0900<br />
Commit id: e3faba5989703e85f6613385b677c3b553a30799<br />
yassai_identifier: removed duplicated output in the manual page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-27 11:18:44 +0900<br />
Author date: 2013-02-27 11:18:44 +0900<br />
Commit id: 282637e882f92b733b3bf6f155f904fe5702a352<br />
Systematically load accessory data; convert factors to characters.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:51:05 +0900<br />
Author date: 2013-02-26 19:51:05 +0900<br />
Commit id: 59b6461d172c6d58345c98defb2456e1fac7debb<br />
Uncompressed the data files.<br />
(Some were actually not compressed).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-02-26 18:36:36 +0900<br />
Commit id: c9130ebc1a6e53015c8f342d9bd381e03f4feba8<br />
Deleted 'dontrun' instruction.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-02-26 18:35:38 +0900<br />
Commit id: b8ee044d9034900cc686ac2d4a7ec8117f0cd47c<br />
Replaced '.' by '_' in function names to avoid confusion with S3 dispatches.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-02-26 17:06:30 +0900<br />
Commit id: 0d6cb9aca3774b97e615428e34c0f3a6006dba46<br />
Renamed functions to replace '.' by '_' and avoid confusion with S3 dispatches.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-02-26 16:59:55 +0900<br />
Commit id: 7e22515d9e8676aaff8a9bd98fa062b8106829be<br />
Renamed ChangeLog to NEWS.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-02-26 16:51:46 +0900<br />
Commit id: fe8d8f98117e578ac5342b54edb9a7533f6865cb<br />
Ensured entries are regular expressions.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-02-26 16:50:08 +0900<br />
Commit id: a080dd9bb390c0c11fef3c4288f4d05f7cc35671<br />
Corrected a typo.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-02-26 19:04:47 +0900<br />
Author date: 2013-01-31 17:57:46 +0900<br />
Commit id: c89cd64950677f13a7c0e9ff4fd3e678ecde279b<br />
Moved installation instructions in a separate page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 15:52:19 +0900<br />
Author date: 2013-01-31 15:52:19 +0900<br />
Commit id: 1a6fcf9f4afa20602333d73386ba3df1c16cd8af<br />
Ignore markdown pages and stylesheets.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 15:33:37 +0900<br />
Author date: 2013-01-31 15:33:37 +0900<br />
Commit id: 85f09c908e98fc82135402f8f18b77201625fc46<br />
Merged READMEs.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 15:32:28 +0900<br />
Author date: 2013-01-31 15:32:28 +0900<br />
Commit id: c276efdec658cd390cf95e51d1dad9408b5070b3<br />
Symbolic link for ikiwiki only.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 15:06:56 +0900<br />
Author date: 2013-01-31 15:06:56 +0900<br />
Commit id: 43b020942234862c7faf6aa9fe2773280dccc97d<br />
Renamed README to comply with Bioconductor.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 15:05:23 +0900<br />
Author date: 2013-01-31 15:05:23 +0900<br />
Commit id: 0e945d7a1751661908b94553e537ec30fbd0ccc8<br />
Normalised parameters, using "data=", like in many other R functions.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 15:03:40 +0900<br />
Author date: 2013-01-31 15:03:40 +0900<br />
Commit id: e323ec8cd505b1ca9057810a1e9ec656c432d261<br />
Replaced unidentified white character by ASCII space.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 14:57:53 +0900<br />
Author date: 2013-01-31 14:57:53 +0900<br />
Commit id: 41d662541c2ab7734f6cee248db723613c65ae98<br />
Do not chose the object called 'clonotypes' by default.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-31 14:57:05 +0900<br />
Author date: 2013-01-31 14:49:11 +0900<br />
Commit id: 10e8717eb6c81c331a2381b93c2a3fe8537de4e9<br />
Merge branch 'master' of git+ssh://osc-lm/osc-fs_home/plessy/git/R/clonotypeR<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 20:38:26 +0900<br />
Author date: 2013-01-08 20:38:26 +0900<br />
Commit id: 48c9fa1f8ab9a7457c7b579c41bded434cd14325<br />
Mention http://clonotyper.branchable.com/<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 20:16:27 +0900<br />
Author date: 2013-01-08 20:16:27 +0900<br />
Commit id: 74925abe92ed7682b56afeb749242aff027def2c<br />
Comment on why the version number starts at 0.99.1.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 20:04:24 +0900<br />
Author date: 2013-01-08 20:04:24 +0900<br />
Commit id: 5fbd8273a36f679032ea615c35b10ecc298aec85<br />
Added biocViews.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 20:00:42 +0900<br />
Author date: 2013-01-08 20:00:42 +0900<br />
Commit id: f304198cf85e7b0546dc4defb68746d03ded0991<br />
Removed file that looks commited by accident.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 19:52:51 +0900<br />
Author date: 2013-01-08 19:52:51 +0900<br />
Commit id: 948e022dcc62643c99a41691e75485dfbca96ae0<br />
Corrected argument name that was too short.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 19:51:51 +0900<br />
Author date: 2013-01-08 19:47:09 +0900<br />
Commit id: 06d1e32a7b6e0fd8bebbc109c9c3caa508599ec0<br />
Notes for the review in Bioconductor.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 19:51:50 +0900<br />
Author date: 2013-01-08 19:43:32 +0900<br />
Commit id: 37298f964077bd147e58052dcf379ff0e5ba73b0<br />
Systematically convert as character, because it is not expensive.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 15:38:30 +0900<br />
Author date: 2012-12-20 21:14:34 +0100<br />
Commit id: dac237885150db368a81e979959011f6f440bfef<br />
Corrected capitalisation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 15:38:30 +0900<br />
Author date: 2012-12-20 11:12:16 +0100<br />
Commit id: 88802f5697838f99b84d74d69617428285d42d68<br />
Also ignore the makefile.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 15:31:20 +0900<br />
Author date: 2013-01-08 15:31:20 +0900<br />
Commit id: d466ad34a6918d42f9fb04c836fd9a6e2dbc2a5b<br />
Explanations about the full source being at git://clonotyper.branchable.com/.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 15:25:06 +0900<br />
Author date: 2013-01-08 15:18:03 +0900<br />
Commit id: 898e169b28fddc6d6fd82536849d18473d58761b<br />
Remove more directories from the Bioconductor package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 15:25:05 +0900<br />
Author date: 2013-01-08 15:12:21 +0900<br />
Commit id: e93ddb3b48e86a7cdf4353a01ab1721e5bf06dd9<br />
Leaner Bioconductor package, without the wiki documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 14:37:36 +0900<br />
Author date: 2013-01-08 14:37:36 +0900<br />
Commit id: 0c2e008f00ee7f7b5e2e1c652fba18c7f00c0ece<br />
Separate .gitignore and .Rbuildignore, to make the Bioconductor package leaner.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 14:34:28 +0900<br />
Author date: 2013-01-08 14:34:28 +0900<br />
Commit id: 45ed4234f5aa4569d871e7320ac310da66285608<br />
Changes forgotten on RIKEN's computer at the end of December.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2013-01-08 14:26:38 +0900<br />
Author date: 2013-01-08 14:26:38 +0900<br />
Commit id: 5edd776656a5f465f834e6ac214a61cc02bf6ee2<br />
Version 0.99.0 according to Bioconductor's guidelines.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-12-16 14:32:05 +0100<br />
Author date: 2012-12-16 14:32:05 +0100<br />
Commit id: 13df713cc992a4882d2e5980d8a39848c7a1039e<br />
Added a one-page vignette pointing at the website.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-12-16 14:26:28 +0100<br />
Author date: 2012-12-16 14:21:21 +0100<br />
Commit id: 5ab860942ffe79aba6baca2b913b4ad6625c7dc1<br />
Removed the function zzz.R supposed to preload support data for yassai.identifier().<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-12-16 12:07:50 +0100<br />
Author date: 2012-12-16 12:07:50 +0100<br />
Commit id: 436a2e1042b9e9ca73abd1fe7d7c24e0ebaf413d<br />
Corrected syntax error in a stop() command.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-12-15 17:23:36 +0100<br />
Author date: 2012-12-15 17:23:36 +0100<br />
Commit id: 9f12d2674c9487be789031053c8a0b0e9b26beeb<br />
Delete accidentally committed swap file.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-12-15 17:10:45 +0100<br />
Author date: 2012-12-15 17:10:45 +0100<br />
Commit id: 3f6bfeae88b74151549842a8c1ae9dc2ef8ea318<br />
Conversion from SRA format (NCBI)<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-12-05 10:23:44 +0000<br />
Author date: 2012-12-05 10:23:44 +0000<br />
Commit id: 7e2b740f7d04e8d104922e3a236b54c3528d4e1e<br />
Replaced another occurence of "Improductive".<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-15 23:07:33 +0900<br />
Author date: 2012-11-15 23:07:33 +0900<br />
Commit id: 51de60575e84883082d0b5e148f805d37eae84de<br />
clonotype.table: do not require the presence of score and mapq columns.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-15 21:27:02 +0900<br />
Author date: 2012-11-15 21:27:02 +0900<br />
Commit id: fae965441114dca1419418a64c98ea3354c840a4<br />
read.clonotypes: added a scores argument to load legacy data.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-15 21:16:59 +0900<br />
Author date: 2012-11-15 21:16:59 +0900<br />
Commit id: 5686598591cfdf104e69930ef06220290f3dbaf0<br />
Renamed yassai.nomenclature yassai.identifier.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-14 15:21:30 +0900<br />
Author date: 2012-11-14 15:21:30 +0900<br />
Commit id: ae5da6c7620ffa7058099e44aec177d2be5f2126<br />
yassai.nomenclature: convert vector to data frame and check presence of appropriate names.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-14 15:08:50 +0900<br />
Author date: 2012-11-14 15:08:50 +0900<br />
Commit id: 16778f15548db144b84f1d4bb99fccfd2d6650b0<br />
yassai.nomenclature: change default data and parameter name.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-14 15:04:54 +0900<br />
Author date: 2012-11-14 15:04:54 +0900<br />
Commit id: 9ebffb23af76ad68628f8ce04737c6bc9ff03980<br />
is_unproductive: new function taken out from read.clonotypes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-14 11:14:03 +0900<br />
Author date: 2012-11-14 11:01:15 +0900<br />
Commit id: a8745080db4508670e2202f1df9e7a57269b6fbc<br />
R script to ensure a proper class for the columns of the clonotypes data frame.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-11-14 10:32:11 +0900<br />
Author date: 2012-11-14 10:32:11 +0900<br />
Commit id: 663089c363eeb2dc6f5ad1ce2906308adb157ee2<br />
rename doc/examples/with__95__test__95__data.mdwn to doc/examples/with_test_data.mdwn<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-11-05 09:58:20 +0000<br />
Author date: 2012-11-05 09:58:20 +0000<br />
Commit id: d40f85b6e358ddb8a827434445d621298314bcae<br />
update for rename of doc/example.mdwn to doc/examples/with__95__test__95__data.mdwn<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-11-05 09:57:25 +0000<br />
Author date: 2012-11-05 09:57:25 +0000<br />
Commit id: ca7e604f9383280b3c7747cba6a61f4156baf51b<br />
rename doc/example.mdwn to doc/examples/with__95__test__95__data.mdwn<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-11-05 09:57:25 +0000<br />
Author date: 2012-11-05 09:57:25 +0000<br />
Commit id: 969aabaf80be8309c49016b20de23818a4594b49<br />
Add a link to the tips.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-11-05 09:05:26 +0000<br />
Author date: 2012-11-05 09:05:26 +0000<br />
Commit id: e3596fde1a53d33d2a918d27a8814e9b7f53645a<br />
Homogenize typography.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 20:48:36 +0900<br />
Author date: 2012-10-10 20:48:36 +0900<br />
Commit id: 44b92e4fce8bd95671ad4ecf30be21ea0bebc4cf<br />
Link to J_before_FGxG and V_after_C.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 20:47:07 +0900<br />
Author date: 2012-10-10 20:47:07 +0900<br />
Commit id: a3e8745ba39a0732979afbea7ea0876f16b4e98b<br />
Documented V_after_C and J_before_FGxG.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 20:44:22 +0900<br />
Author date: 2012-10-10 20:44:22 +0900<br />
Commit id: 6f1ce7e778394062e3f9f5d684bec298fd2b4559<br />
Added an alias for the codon_ids table.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 20:32:16 +0900<br />
Author date: 2012-10-10 20:32:16 +0900<br />
Commit id: 80a15c8ef6de3a12bd9fd2a978ec74ddc901bc0a<br />
Refreshed HTML documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 20:27:18 +0900<br />
Author date: 2012-10-10 20:27:18 +0900<br />
Commit id: 5e875c51623030840d62a7126c604601a9c1bc18<br />
Renamed html html_doc to avoid a warning.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 20:00:28 +0900<br />
Author date: 2012-10-10 19:56:56 +0900<br />
Commit id: 3b7f393ee667f93a047558ed9301012beb0d0393<br />
Exclude multi-megabyte example data from the R package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 19:38:40 +0900<br />
Author date: 2012-10-10 19:38:40 +0900<br />
Commit id: 4617fab37a16d1a3ed4154b866515d3b5a760616<br />
Added a changelog (GNU-style).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 18:56:30 +0900<br />
Author date: 2012-10-10 18:56:30 +0900<br />
Commit id: 702bfc4f59e331c3c9fa797d196dfc969870e856<br />
Corrected Frenglish “improductive” with “unproductive”.<br />
This can break backwards compatibility.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 18:55:11 +0900<br />
Author date: 2012-10-10 18:55:11 +0900<br />
Commit id: 284902d16b5c040f0d56577642a851b7c408976c<br />
Corrected typo.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-10-10 18:49:15 +0900<br />
Author date: 2012-10-10 18:25:58 +0900<br />
Commit id: 322a12f4bd1a583fa72984439120c2a8d97dcf63<br />
Tip: Reverse-complement and append mate-pair sequence to the first read<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-10-09 11:35:00 +0000<br />
Author date: 2012-10-09 11:35:00 +0000<br />
Commit id: a02891f1fef7e36843b8b049b6d4616b65446302<br />
To do: Report the number of V segments found after `clonotypeR detect`.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-10-09 11:22:11 +0000<br />
Author date: 2012-10-09 11:22:11 +0000<br />
Commit id: f2dcc5971b58d68b95d3279ca70be81c8064c903<br />
Link to source archive in the git repository (branch « release »).<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-09-06 10:38:39 +0000<br />
Author date: 2012-09-06 10:38:39 +0000<br />
Commit id: 06f61655c82aa5261a82c6645d81fde5322904f7<br />
Changed version number (R requires integers), and corrected installation instructions.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-09-06 19:25:48 +0900<br />
Author date: 2012-09-06 19:25:48 +0900<br />
Commit id: a180ec1a79acf71f837dba43e07750e0512d9315<br />
Current version at the time of first submission.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-09-06 19:14:21 +0900<br />
Author date: 2012-09-06 19:14:21 +0900<br />
Commit id: c178971ed2687a8aab4151bbbd79fad0d25551d5<br />
Link to gallery with thumbnails.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-09-06 06:51:35 +0000<br />
Author date: 2012-09-06 06:51:35 +0000<br />
Commit id: fb339a75a2760ddcce0606e5a969a44958260f53<br />
Gallery page.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-09-06 06:45:32 +0000<br />
Author date: 2012-09-06 06:45:32 +0000<br />
Commit id: 48316a2d65dac58420c2240c5e0730933d1fabb4<br />
Corrected name.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-09-06 15:28:43 +0900<br />
Author date: 2012-09-06 15:28:43 +0900<br />
Commit id: e22135b6dc898713766d7881091cffed2a3c7e7b<br />
Thumbnails<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-09-06 15:27:53 +0900<br />
Author date: 2012-09-06 15:27:53 +0900<br />
Commit id: ba6bbfd3b766c4528dc2479e7f415fd07a27c2b7<br />
Example output files from R.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-09-06 15:18:22 +0900<br />
Author date: 2012-09-06 15:18:22 +0900<br />
Commit id: df014b0aed6b1c424c10c1fc441da346ad27edd8<br />
Installation from source.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-09-06 05:45:59 +0000<br />
Author date: 2012-09-06 05:45:59 +0000<br />
Commit id: 0a192aff326956d64578ad40d33fd68cfa4ae2e5<br />
Indicate the name of the unknown libaries.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-09-04 14:36:24 +0900<br />
Author date: 2012-09-04 14:36:24 +0900<br />
Commit id: 5926af361e73ace48ac790e2ff75f6102e54d347<br />
3,653 V–J pairs were detected in SRR407172.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-11 10:44:02 +0000<br />
Author date: 2012-08-11 10:44:02 +0000<br />
Commit id: 9d0226640e2a930a0bc7fb0100cced0837b8c8a8<br />
Suggest pvclust.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-11 17:38:32 +0900<br />
Author date: 2012-08-11 17:38:32 +0900<br />
Commit id: 931fc14f0f83dc5de39a86b7e791032bb324a213<br />
Filter out reads with low mapping quality and alignment scores.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-10 22:13:27 +0900<br />
Author date: 2012-08-10 22:12:13 +0900<br />
Commit id: 6158d7b93dc57d6edd3390c9977a6409ecf510b8<br />
Removed mention of clonotyper convert.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-10 03:50:37 +0000<br />
Author date: 2012-08-10 03:50:37 +0000<br />
Commit id: 464080b5d6c02cdd7c0acd28b9f102ebaf1cd473<br />
Work in /home/ubuntu/clonotyper.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-10 03:50:01 +0000<br />
Author date: 2012-08-10 03:50:01 +0000<br />
Commit id: 6263579ee80b80442b6f5ca0bd3a271489fdb572<br />
Link to /mnt, and added a warning.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-10 03:48:33 +0000<br />
Author date: 2012-08-10 03:48:33 +0000<br />
Commit id: 30ef03fd9863082955e0a5d4bd0753626f3e5c23<br />
Document score and mapq columns.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-10 09:54:06 +0900<br />
Author date: 2012-08-10 09:53:34 +0900<br />
Commit id: 1f461943a713cfa8f9a8b8095a14fb6545c1664d<br />
Users not in the group staff need administrator priviledges.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-09 22:46:44 +0000<br />
Author date: 2012-08-09 22:46:44 +0000<br />
Commit id: 563284305b499452309164cfc0c46ab92eb9ce52<br />
Do not load sequences as factors.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 14:54:59 +0900<br />
Author date: 2012-08-09 14:54:59 +0900<br />
Commit id: c4e488154eec177bfa037581369aa95b3325ff7e<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 14:08:24 +0900<br />
Author date: 2012-08-09 14:08:24 +0900<br />
Commit id: 159b21792b0845462cb13e47e7a0f79364cad990<br />
Suggest vegan.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 14:04:47 +0900<br />
Author date: 2012-08-09 14:04:47 +0900<br />
Commit id: d3b4a62dd7cf418ac93f364ca82f6b2dd759a9cf<br />
No need for pandoc in this example. Do not note twice that instance storage is mounted in /mnt. Remove timestamps.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-09 05:04:12 +0000<br />
Author date: 2012-08-09 05:04:12 +0000<br />
Commit id: 4c51296f717e3fa201eb3da71ff61e455d81ad33<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 13:44:06 +0900<br />
Author date: 2012-08-09 13:44:06 +0900<br />
Commit id: 9727ed496024a33f0851f2a9a8211b53b2f4d1ae<br />
How to build and install the clonotypeR R package from the Git clone.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-09 04:44:46 +0000<br />
Author date: 2012-08-09 04:44:46 +0000<br />
Commit id: 2514e4d01f4326fcf1bf70d3a5161774deb19e7b<br />
Compress the segment sequence files.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 13:26:34 +0900<br />
Author date: 2012-08-09 13:26:34 +0900<br />
Commit id: 21ae3c1ccc3f0f51e199a38aea7ea664858d58a8<br />
Segment data for R, and mechanism to refresh it. This needs Bioconducor's Biostrings package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 13:19:41 +0900<br />
Author date: 2012-08-09 13:19:41 +0900<br />
Commit id: 53004ed4a20f35b0859e83483ceefd515de8e6c8<br />
module → package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 13:08:10 +0900<br />
Author date: 2012-08-09 13:08:10 +0900<br />
Commit id: 960b90f5e5a37a62b0da374d39c39410c6d23d2b<br />
Change the mechanism that provides segment data in R, to avoid run-time dependance on Biostrings.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-09 13:02:27 +0900<br />
Author date: 2012-08-09 11:43:55 +0900<br />
Commit id: 3158e88845e3a8b87e75d865e35cd9eb8098974f<br />
Build the R module of *clonotypeR*.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-09 00:10:35 +0000<br />
Author date: 2012-08-09 00:10:35 +0000<br />
Commit id: 32af088c165b4b4c009d7098792b82b998d526c8<br />
Link to instructions to convert FASTQ files, outline of analysis in R.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 08:53:03 +0000<br />
Author date: 2012-08-08 08:53:03 +0000<br />
Commit id: 4cdc78d3d250a5427b834fbb6f74ff1b23376ea9<br />
Download and use sff_extract to convert the 454 SFF files.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 08:50:09 +0000<br />
Author date: 2012-08-08 08:50:09 +0000<br />
Commit id: ca6915ec03752d8a90f3f6ee296161b62d37225d<br />
sff_extract is now recommended but not required.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 08:48:26 +0000<br />
Author date: 2012-08-08 08:48:26 +0000<br />
Commit id: 5950e562b5ce019b71b0b8a6d6901a342567a6ce<br />
How to convert many AB1 files in a single FASTQ file.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 07:51:36 +0000<br />
Author date: 2012-08-08 07:51:36 +0000<br />
Commit id: 457214be1be8133574ab98cd362464ed161e5c19<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 07:47:12 +0000<br />
Author date: 2012-08-08 07:47:12 +0000<br />
Commit id: d4c17bf9c5f0c90206bc8232f4d3adc99f787f9d<br />
Postpone development of conversion command.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 16:03:28 +0900<br />
Author date: 2012-08-08 16:03:28 +0900<br />
Commit id: 27764d3d29a491a2052aa1f195ab714fffca3baf<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 16:00:50 +0900<br />
Author date: 2012-08-08 16:00:50 +0900<br />
Commit id: 21337966a854f79522db90c29132ef69591481d4<br />
Update manpage.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 07:01:31 +0000<br />
Author date: 2012-08-08 07:01:31 +0000<br />
Commit id: e592ed9f63e8047d1a229f7bf98c336556062c70<br />
Remove double quotes, to allow processing more than one file (with no spaces in the name).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 15:57:41 +0900<br />
Author date: 2012-08-08 15:57:41 +0900<br />
Commit id: 7127f9a60d238c7d9d6f30d0ac1b2e7a7f7be958<br />
Postponed the development of a conversion command.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-08 06:49:15 +0000<br />
Author date: 2012-08-08 06:49:15 +0000<br />
Commit id: 92c5e1ecab616956085d515371d9df9ccf80c031<br />
Give up parsing single clonotypes for the moment, and update documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 15:17:46 +0900<br />
Author date: 2012-08-08 15:17:46 +0900<br />
Commit id: 55819b5e99a2c2a871542295012e1e977caf945a<br />
Updated example to contain alignment scores and mapping qualities.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 15:05:07 +0900<br />
Author date: 2012-08-08 15:05:07 +0900<br />
Commit id: 4665683767030eaf441918a0297c9ffd71cb0569<br />
Use standard names for segments that has a counterpart that was removed.<br />
For instance, TRAV7N-5_7D-5 is reverted to TRAV7N-5.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 14:52:26 +0900<br />
Author date: 2012-08-08 14:52:26 +0900<br />
Commit id: fe58ce50dd0f301e55d89714e7bb10c9c14cc56b<br />
Convert to character if necessary.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-08 07:42:22 +0900<br />
Author date: 2012-08-08 07:42:22 +0900<br />
Commit id: 2bc1420b180a897dc45d69feff4a1a714f2e3890<br />
Done in commit 7cf11805d84ff8dc6a537c17e73efa275077915d.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-07 11:14:39 +0000<br />
Author date: 2012-08-07 11:14:39 +0000<br />
Commit id: 943dbeb9c433a9d0857e440934ebad63131bfcc3<br />
Created a shortcut for commits.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-07 11:13:20 +0000<br />
Author date: 2012-08-07 11:13:20 +0000<br />
Commit id: b4fb181e9402fadbe60e33064b213996f887ab34<br />
Documentation updates.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-07 20:00:01 +0900<br />
Author date: 2012-08-07 20:00:01 +0900<br />
Commit id: cd8789b3b1ca5eb8b0ff9ca74b873632c834f45a<br />
Accept alignment scores and mapping qualities.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-07 19:53:21 +0900<br />
Author date: 2012-08-07 19:53:21 +0900<br />
Commit id: 3b762f51300af2e5760630f35d01e3842242048d<br />
Corrected and vectorised yassai.nomenclature.R.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-07 19:39:10 +0900<br />
Author date: 2012-08-07 19:39:10 +0900<br />
Commit id: 7cf11805d84ff8dc6a537c17e73efa275077915d<br />
Convert names of V and J segments in yassai.nomenclature().<br />
Closes: 87de09572d8ed59646625d2929b88bce1a3f691b<br />
Closes: yassai.nomenclature_returns_incorrect_values.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-06 21:16:22 +0900<br />
Author date: 2012-08-06 21:16:22 +0900<br />
Commit id: 7484c392a39c5a13e23274dad6c778fbc59ea6d1<br />
Replace hardcoded column names by their name.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-06 21:07:05 +0900<br />
Author date: 2012-08-06 21:06:47 +0900<br />
Commit id: 5b5498fd65be98f69e3954a20a78cbdbd5081d2e<br />
Extract and detect clonotypes from GSE35626.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-05 03:11:40 +0000<br />
Author date: 2012-08-05 03:11:40 +0000<br />
Commit id: 219d9df718d33a5b28b92e43aae5655312931411<br />
Instructions to run from git clone will be completed later.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-05 03:06:29 +0000<br />
Author date: 2012-08-05 03:06:29 +0000<br />
Commit id: 2d724f12fda97d167bb5894d3c783d5d64dfb606<br />
Added back pseudogenes, polished alignment, rebuilt derived files.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-05 12:05:14 +0900<br />
Author date: 2012-08-05 12:04:16 +0900<br />
Commit id: 7e84f7c766a4eb429a9e731cbe89198a50925d40<br />
Added back TRAV6D-6 and TRAV6N-6 as they are unique, explain about removals.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-05 12:05:14 +0900<br />
Author date: 2012-08-05 09:32:45 +0900<br />
Commit id: cb88320627458f0e54be47dbd80dfec20ad91754<br />
Install clonotyper from source in /mnt.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 23:49:26 +0000<br />
Author date: 2012-08-04 23:49:26 +0000<br />
Commit id: 84a978afa19dcdaee718474e5384988b5d0f21be<br />
Inserted a table of contents.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 13:09:17 +0000<br />
Author date: 2012-08-04 13:09:17 +0000<br />
Commit id: 46312bacdbebe13f8ef9e73fec5066a08f42bb8b<br />
Convert from SRA to FASTQ format with the SRA Toolkit.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 13:06:56 +0000<br />
Author date: 2012-08-04 13:06:56 +0000<br />
Commit id: d775e894f2447be67b010d3fe3691d7e988afd8e<br />
Record all mapping qualities and alignment scores instead of discarding low ones.<br />
The scores are temporarly embedded in the read names. The filtering will take<br />
place in R with the function "clonotype.table".<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-04 21:54:36 +0900<br />
Author date: 2012-08-04 21:54:36 +0900<br />
Commit id: 6ee0d196cac21307a36bdf41c896cb33d2d62b9e<br />
Pass CLONOTYPER_REFERENCE to VJsplit.<br />
VJsplit and clonotypeR should rather be merged.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-04 21:51:10 +0900<br />
Author date: 2012-08-04 21:51:10 +0900<br />
Commit id: c6967a6fdea7d9f270fd3814a407ffa0f727478f<br />
Do not set CLONOTYPER_REFERENCE in VJsplit if absent.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-04 21:50:39 +0900<br />
Author date: 2012-08-04 20:51:26 +0900<br />
Commit id: 49370c4b6ef91b1397c7ab0b9701965ea6ef33dd<br />
Really count the number of V segments detected.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 12:07:17 +0000<br />
Author date: 2012-08-04 12:07:17 +0000<br />
Commit id: 30a6c55210e2c095adb32337064e4aebd601bf8b<br />
Look for scripts and reference alignments in fixed locations where no path is provided.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-04 20:48:49 +0900<br />
Author date: 2012-08-04 20:48:49 +0900<br />
Commit id: cdb630e18dfa3c9edef57f9205773c00a1235366<br />
create a directory for analysis in /mnt, where the instance storage is mounted.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 11:46:17 +0000<br />
Author date: 2012-08-04 11:46:17 +0000<br />
Commit id: 7f5722071879eedf1427bcf3d7145ff8c58debb9<br />
Startyed example analysis using the GSE35626 public dataset.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 09:35:55 +0000<br />
Author date: 2012-08-04 09:35:55 +0000<br />
Commit id: 659686f92e6b0b22ea3fb9188ae8da67f752b6b4<br />
Example analysis using the GSE35626 public dataset.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 09:18:17 +0000<br />
Author date: 2012-08-04 09:18:17 +0000<br />
Commit id: 0ac53483220ff1153b67e6d1a2aa3e2ced726384<br />
Link to the example with the GSE35626 dataset.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-08-04 09:15:57 +0000<br />
Author date: 2012-08-04 09:15:57 +0000<br />
Commit id: f2a41806b5e2f25113b788508d2c3b8a37909a3c<br />
Document what common_clonotypes does on a single group of samples.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-03 18:18:54 +0900<br />
Author date: 2012-08-03 18:18:54 +0900<br />
Commit id: 32f81615ac4de2c7240c2f7058d3a8689845343d<br />
Typo.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-03 15:34:00 +0900<br />
Author date: 2012-08-03 15:34:00 +0900<br />
Commit id: 8e4caeb05e7a4a628c21c6b9338528c68fdea50a<br />
Refreshed R documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-03 15:27:31 +0900<br />
Author date: 2012-08-03 15:27:31 +0900<br />
Commit id: ccbeb8f84a147c49e883d83b93e7c2293585ac5f<br />
Example on how to count clonotypes common to two groups of libraries.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-03 15:26:41 +0900<br />
Author date: 2012-08-03 15:26:41 +0900<br />
Commit id: deec7882c6975b93c6f3bc663031e2c60f8a3dd5<br />
Use all libraries of the clonotypes data frame by default.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-02 11:02:39 +0900<br />
Author date: 2012-08-02 11:02:39 +0900<br />
Commit id: 4ce04656c3321fa05d1956ff484d85ea3259d2af<br />
Specify the field separator.<br />
This allows empty 'peptide' values, when the CDR3 is shorter than 3 bases.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 16:06:31 +0900<br />
Author date: 2012-08-01 16:06:31 +0900<br />
Commit id: 2253562b4dd5303c5da536c1bd29c0653e8fdb79<br />
Skip header only for OSCTable files (TSV files do not have).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 16:01:14 +0900<br />
Author date: 2012-08-01 16:01:14 +0900<br />
Commit id: 8fbcb6e1093b65a1ed476ef94915f817320b8145<br />
Ignore nonexistent files.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 12:48:19 +0900<br />
Author date: 2012-08-01 12:48:19 +0900<br />
Commit id: 5bd8c70d573dfc79bdf67d13a296a2b9f2ec3576<br />
Honor TMPDIR.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 11:50:22 +0900<br />
Author date: 2012-08-01 11:50:22 +0900<br />
Commit id: 8973ddc350becf57220e31efc63035762fa17b0a<br />
Use the correct directory for cleaning the clonotype file.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 11:42:35 +0900<br />
Author date: 2012-08-01 11:42:35 +0900<br />
Commit id: 647aa419a5332b49b64f9d6e919f15d0007abc4e<br />
Added a DEBUG option, and reduce the number of temporary files when not using it.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 11:37:48 +0900<br />
Author date: 2012-08-01 11:37:48 +0900<br />
Commit id: ef1efab3236e2080e4df5e635a4933dbbb31f9ef<br />
Transfer a comment to the tips page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-08-01 11:17:04 +0900<br />
Author date: 2012-08-01 11:17:04 +0900<br />
Commit id: 423cf824e3b9788c732c488440d3204949bcfa48<br />
Extend common_clonotypes with a matrix mode.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-25 19:50:15 +0900<br />
Author date: 2012-07-25 19:50:15 +0900<br />
Commit id: f1bfc0d7c8eef54f18898057fdf812b7d4d8acc4<br />
Reorganised the clonotype page, giving an example ane clarifying that the C and FGxG motif are not included.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-25 05:11:12 +0000<br />
Author date: 2012-07-25 05:11:12 +0000<br />
Commit id: 828365468658f5307b6dd08ccbc553cd438490f3<br />
Link to the reference directory's README page.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-25 04:49:01 +0000<br />
Author date: 2012-07-25 04:49:01 +0000<br />
Commit id: b41c10020484c0bf65611f96bfab3ecd7b5bab4a<br />
Polish the reference directory's README.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-25 13:45:43 +0900<br />
Author date: 2012-07-25 13:45:43 +0900<br />
Commit id: db8aff192824b7e5c0d9c4770c97c9ee7c0c828c<br />
Removes dependance on moreutils by replacing the call to sponge.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-25 13:30:28 +0900<br />
Author date: 2012-07-25 13:30:28 +0900<br />
Commit id: e03a112b7e446ecb39ced21d74945f72b110d2e3<br />
Moved FASTQ conversion instructions to the clonotypeR script.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-25 11:49:40 +0900<br />
Author date: 2012-07-25 11:49:40 +0900<br />
Commit id: 91bf372202d1437a8486acc7593bc4323a7ed617<br />
Introduce clonotypes.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 12:45:31 +0000<br />
Author date: 2012-07-24 12:45:31 +0000<br />
Commit id: 00051fe58e0eeb6f149e0ce2d5f5a7cf6756a1b5<br />
Link to clonotype page.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 12:40:59 +0000<br />
Author date: 2012-07-24 12:40:59 +0000<br />
Commit id: fbbd3166a535af18b0c5782f8918bc963ebc411c<br />
Background to underline code and examples.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 21:24:35 +0900<br />
Author date: 2012-07-24 21:24:35 +0900<br />
Commit id: 04f0d2e87b2faf19bc940363b17d5785103c8630<br />
Merge branch 'master' of ssh://clonotyper.branchable.com<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 21:02:15 +0900<br />
Author date: 2012-07-24 21:02:15 +0900<br />
Commit id: 380e1089011f44655d168fca132494d4c007e857<br />
Data exploration in R.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 11:56:38 +0000<br />
Author date: 2012-07-24 11:56:38 +0000<br />
Commit id: 41c326181660ea9ca29a22ad42117e41102e6dc9<br />
List Biostrings in the requirements.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 11:21:24 +0000<br />
Author date: 2012-07-24 11:21:24 +0000<br />
Commit id: aee84935a807a53ebb2347a37858cba816398673<br />
Convenience target to build the R module.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 20:16:14 +0900<br />
Author date: 2012-07-24 20:16:14 +0900<br />
Commit id: 9a113329a4116a5bb16531a153ae01f254d4f70f<br />
Ignore Git and Ikiwiki directories when building the R module.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 20:15:37 +0900<br />
Author date: 2012-07-24 20:15:37 +0900<br />
Commit id: 34a33012d0878dfcb4de8691171ecb9387fbc58c<br />
Convenience target to call R CMD check.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 20:13:22 +0900<br />
Author date: 2012-07-24 20:13:22 +0900<br />
Commit id: 50dc075faad81c82b2a0d00f00a96bf54c722ffc<br />
Stop on error.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 20:05:16 +0900<br />
Author date: 2012-07-24 20:05:16 +0900<br />
Commit id: 8109542596b9b1982495f023c769616bc94cb385<br />
Default location for reference files, create clonotype directory if it does not exist.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 20:03:14 +0900<br />
Author date: 2012-07-24 20:03:14 +0900<br />
Commit id: bd429351a7e929b0b8efd87d0002d602d3306c1f<br />
Miniaturise whole page header.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 19:03:05 +0900<br />
Author date: 2012-07-24 19:03:05 +0900<br />
Commit id: 49d8d5a5071ff575ca9916954a89ffaef199d100<br />
Make the branchable action bar less visible.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 18:52:29 +0900<br />
Author date: 2012-07-24 18:52:29 +0900<br />
Commit id: fff2a99b1788ea2215284852c4137a263155df09<br />
Removed subtitle.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 09:37:46 +0000<br />
Author date: 2012-07-24 09:37:46 +0000<br />
Commit id: 1762c0cda5668924b405fc324ed8f685c0a5b0d5<br />
Mention alternative works.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 09:35:15 +0000<br />
Author date: 2012-07-24 09:35:15 +0000<br />
Commit id: 80b51287b661c50293f22c2341ffa0f87290dc23<br />
Create directories if they do not already exist.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-24 09:28:28 +0000<br />
Author date: 2012-07-24 09:28:28 +0000<br />
Commit id: afab0c906ef95097fe5cf41669e07d3685a64fd6<br />
Create $EXTRACT_DIR instead of stopping with an error if it is absent.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-24 18:25:21 +0900<br />
Author date: 2012-07-24 18:25:21 +0900<br />
Commit id: 8c13182f552c00c4dcd808c0317e9135dcb115e3<br />
Transfer instructions from README to doc.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 21:55:04 +0900<br />
Author date: 2012-07-23 21:55:04 +0900<br />
Commit id: ecf7151fa47931e4bf6df118606c2762404d8181<br />
Example analysis.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 21:48:48 +0900<br />
Author date: 2012-07-23 21:48:48 +0900<br />
Commit id: 110e5fc8c8a102b59dde301df45f27ed54d620c1<br />
Link to example and manual page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 21:47:35 +0900<br />
Author date: 2012-07-23 21:45:31 +0900<br />
Commit id: 62309082cc3d5f2d6cdff29d8a5b3b03d84ff6cf<br />
Draft manual page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 21:40:57 +0900<br />
Author date: 2012-07-23 21:37:56 +0900<br />
Commit id: 72edf13c5416d873a716a82ab0156c68db4cea2c<br />
VJsplit: do not output the sequence passed to vectorstrip.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 21:35:18 +0900<br />
Author date: 2012-07-23 21:35:18 +0900<br />
Commit id: ff0a39ea2a4082ec0bbf0ab107556a50f300de80<br />
Turn off verbosity by default.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 20:21:59 +0900<br />
Author date: 2012-07-23 20:19:43 +0900<br />
Commit id: b824c1f1d358f3a4c6095a63320a7417d03485b6<br />
Test if $EXTRACT_DIR is present.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 20:21:57 +0900<br />
Author date: 2012-07-23 20:19:18 +0900<br />
Commit id: 657b84a11f9d67e9bb0400241c32ea353488b189<br />
Point default paths to /etc and /usr/share.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 19:40:24 +0900<br />
Author date: 2012-07-23 19:40:24 +0900<br />
Commit id: ba7a6d27bf0f5e5c8115742da00679a45beb7745<br />
Moving general documentation to a 'doc' folder.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 18:34:09 +0900<br />
Author date: 2012-07-23 18:34:09 +0900<br />
Commit id: 21e5820be3d6e8b5844161c4f93ea22bb22c920b<br />
Moving general documentation to a 'doc' folder.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-23 18:33:25 +0900<br />
Author date: 2012-07-23 18:33:25 +0900<br />
Commit id: 1624e36c0995d729b6526f66c1e0dfee7c0bba5c<br />
Example data from three 454 runs.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-20 18:30:22 +0900<br />
Author date: 2012-07-20 18:30:22 +0900<br />
Commit id: a6a6aa2d98c1af16420d4d2ef17a67992a93524f<br />
More cosmetic typographical changes.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-20 09:18:43 +0000<br />
Author date: 2012-07-20 09:18:43 +0000<br />
Commit id: 7cf7386f69467833e72cbc53df74d14f4393f67b<br />
Drafted workflow.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-20 08:28:18 +0000<br />
Author date: 2012-07-20 08:28:18 +0000<br />
Commit id: 234b4da7afa24f12c2df65f1ac1b25dd9251385b<br />
Cosmetic typographical changes.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-20 06:58:15 +0000<br />
Author date: 2012-07-20 06:58:15 +0000<br />
Commit id: d3911ac5fa37787e9c9d0f667f00eac037e3930e<br />
Link to create the workflow page.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-20 06:45:40 +0000<br />
Author date: 2012-07-20 06:45:40 +0000<br />
Commit id: 5a3447d6ab8baa1fd804321f17f3cff4762ff3b7<br />
Ignore for R what Git ignores.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-20 13:46:04 +0900<br />
Author date: 2012-07-20 13:46:04 +0900<br />
Commit id: a3da418ec4034eec9248773155714f5d5121d7d8<br />
Link R documentation to home page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-20 13:39:40 +0900<br />
Author date: 2012-07-20 13:39:40 +0900<br />
Commit id: 0cebb909093538b3f27461fd442f1ee137781e4d<br />
HTML documentation of the R package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-20 13:05:44 +0900<br />
Author date: 2012-07-20 13:05:44 +0900<br />
Commit id: 9b3268609cb0d81b8a996d3903bc7f155a8825e1<br />
Build the HTML documentation of the R package.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-20 13:04:57 +0900<br />
Author date: 2012-07-20 13:04:57 +0900<br />
Commit id: a112ecba087d380914f37d7a881cebe7fd42b717<br />
Uppercase Bugs.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-19 19:49:46 +0900<br />
Author date: 2012-07-19 19:49:46 +0900<br />
Commit id: 015ea4901bf9f91ee8342bc063fb83e326c52c11<br />
Moved the page for resolved bugs to the upper-case directory.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-19 19:44:37 +0900<br />
Author date: 2012-07-19 19:44:37 +0900<br />
Commit id: 9b9777f64fc6232d2897453a8175f317de208123<br />
Removed `feedpages="created_after(bugs/no_commit_mails_for_new_pages)"`<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-19 01:49:46 +0000<br />
Author date: 2012-07-19 01:49:46 +0000<br />
Commit id: 87de09572d8ed59646625d2929b88bce1a3f691b<br />
yassai.nomenclature returns incorrect values.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-19 01:48:07 +0000<br />
Author date: 2012-07-19 01:48:07 +0000<br />
Commit id: 457946564a564fc619af23d8ea1287dc4aea4979<br />
Copied from ikiwiki's bugs page.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-19 01:45:21 +0000<br />
Author date: 2012-07-19 01:45:21 +0000<br />
Commit id: 3fdb95c79d1a2062bedcb66918c00ea5879e9c95<br />
Copied from ikiwiki's bugs page.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-19 01:44:23 +0000<br />
Author date: 2012-07-19 01:44:23 +0000<br />
Commit id: 8c26833a69d608a2dd191b887206ecd6fa3d2e78<br />
Added a link to the source code.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-19 01:38:04 +0000<br />
Author date: 2012-07-19 01:38:04 +0000<br />
Commit id: 894c2fd99fdf889525daaca025f3f1b7f7f24ddd<br />
TODO: Support extraction of barcoded reads.<br />
Committed by: admin<br />
Author Name: http://plessy-riken-jp.myopenid.com/<br />
Commit date: 2012-07-19 01:35:50 +0000<br />
Author date: 2012-07-19 01:35:50 +0000<br />
Commit id: 5ccaae9f37ed68069917a74357e703ae252aa57f<br />
Committed by: admin<br />
Author Name: https://www.google.com/accounts/o8/id?id=AItOawnBeKsGItVOjWWGrYqYJDfn0hacxUHE0R4<br />
Commit date: 2012-07-19 01:18:50 +0000<br />
Author date: 2012-07-19 01:18:50 +0000<br />
Commit id: 0b2a08f02fb74a1fce64539906660a0b29274c0f<br />
Committed by: admin<br />
Author Name: https://www.google.com/accounts/o8/id?id=AItOawnBeKsGItVOjWWGrYqYJDfn0hacxUHE0R4<br />
Commit date: 2012-07-19 01:12:48 +0000<br />
Author date: 2012-07-19 01:12:48 +0000<br />
Commit id: 23c7f53c15a984ab80ed6b911bef69cc07721b7a<br />
Corrected a typo.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-18 20:27:22 +0900<br />
Author date: 2012-07-18 20:27:22 +0900<br />
Commit id: dbcf051f8fc0345f298ae348e378f302103bab5b<br />
Place clonotypeR in the public domain.<br />
See: http://creativecommons.org/publicdomain/zero/1.0/<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-18 20:22:42 +0900<br />
Author date: 2012-07-18 20:22:42 +0900<br />
Commit id: 17c160a4224ae3d8f011d8b177a4f70b8e886c83<br />
Index page.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-18 20:10:22 +0900<br />
Author date: 2012-07-18 20:10:22 +0900<br />
Commit id: 44b75a4381e6790186985666f33a10edcaed79ff<br />
Merge branch 'master' of git+ssh://osc-lm/osc-fs_home/plessy/git/clonotypeR<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-18 20:08:24 +0900<br />
Author date: 2012-07-18 20:08:24 +0900<br />
Commit id: fda34793a1a8e8fa5a298e34ec3ac6f6bd04cf6b<br />
Merge /home/plessy/git/clonotypeR<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-18 17:53:48 +0900<br />
Author date: 2012-07-18 17:53:48 +0900<br />
Commit id: 77799de49185890c7ae050b148795f14dcba25ad<br />
initial commit<br />
Committed by: admin<br />
Author Name: admin<br />
Commit date: 2012-07-18 03:56:07 +0000<br />
Author date: 2012-07-18 03:56:07 +0000<br />
Commit id: c3c98e1f1873691a926b21a6c3a193db0691c7b5<br />
Attempt to load codon_ids if not found.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-17 19:36:16 +0900<br />
Author date: 2012-07-17 19:36:16 +0900<br />
Commit id: 65c20abd543e971a49c416c60d7eeeba9a847575<br />
Workaround that actually does not work in the regression tests.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-17 18:56:24 +0900<br />
Author date: 2012-07-17 18:56:24 +0900<br />
Commit id: e2028c44097db1e04b1156c44281637d61bea985<br />
Superseded by data/J_before_FGxG.R and data/V_after_C.R.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-17 18:10:36 +0900<br />
Author date: 2012-07-17 18:10:36 +0900<br />
Commit id: 2eba0f44b76672fb06c050a984bc72ed89496028<br />
Corrected typo in J_before_FGxG.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-07-17 18:04:22 +0900<br />
Author date: 2012-07-17 18:04:22 +0900<br />
Commit id: b8aa6fb7436d6cda6197df5ef62faa5efba05d8a<br />
Corrects a stupid bug. Never write programs in a rush before eating ! Always make tests !<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-14 13:39:25 +0900<br />
Author date: 2012-06-14 13:39:25 +0900<br />
Commit id: 289ca1b13c02db17eed38e00aae33429bd41f1e9<br />
Depends: Biostrings.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-14 11:54:30 +0900<br />
Author date: 2012-06-14 11:54:30 +0900<br />
Commit id: 8e3d4fb21ee98811f064ddf1b9e3a14efa366ad9<br />
Pre-load V_after_C" and "J_before_FGxG". Is that necessary ?<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-14 11:53:45 +0900<br />
Author date: 2012-06-14 11:53:45 +0900<br />
Commit id: 61cb7edfb7a54201319df952155b29f2ccbe181b<br />
Link to common_clonotypes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-14 11:53:28 +0900<br />
Author date: 2012-06-14 11:53:28 +0900<br />
Commit id: a54d69501aa48c80c1d644290563d93dc92776be<br />
common_clonotypes: lists clonotypes common to two groups of samples.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-14 11:49:17 +0900<br />
Author date: 2012-06-14 11:49:17 +0900<br />
Commit id: d6ea4990313a6f222aa2e2ccc840f669180d9b63<br />
Renamed to avoid confusion with generic functions.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-14 11:33:46 +0900<br />
Author date: 2012-06-14 11:33:46 +0900<br />
Commit id: 8dbbc4359b47c8f80da2d3d264b671a76484433c<br />
Load V_after_C and J_before_FGxG file for calculating Yassai's nomenclature.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-12 21:28:35 +0900<br />
Author date: 2012-06-12 21:27:57 +0900<br />
Commit id: 9ca756a7a87dd5fc592783387de6ff2fa82ecdcb<br />
Compressed so that they are found in the same path in the Git repository and the installed R library.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-12 21:07:32 +0900<br />
Author date: 2012-06-12 21:07:32 +0900<br />
Commit id: af1286faff89813f5f853eef96d661350b1cd603<br />
Proofread documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-12 20:53:36 +0900<br />
Author date: 2012-06-12 20:53:36 +0900<br />
Commit id: d350a525f229bab443615e2847be97f9145846df<br />
Renamed to avoid confusion with generic functions.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-12 20:44:15 +0900<br />
Author date: 2012-06-12 20:44:15 +0900<br />
Commit id: 4fc5bb4c2cc97fd7e55e320c3352e479f54d2284<br />
Corrected code/documentation mismatches.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-11 19:01:46 +0900<br />
Author date: 2012-06-11 19:01:46 +0900<br />
Commit id: 3c39536ca0f8921293929342f1c9785786285e48<br />
Document filters option of clonotype.table.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-11 18:52:32 +0900<br />
Author date: 2012-06-11 18:52:32 +0900<br />
Commit id: 7da963bd688f19f13c350759e59ae75590a0783b<br />
Corrections for empty entries.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-11 18:41:20 +0900<br />
Author date: 2012-06-11 18:41:20 +0900<br />
Commit id: 842cbf83f24ddfdc01e38a2904967cb1c667e0cb<br />
Corrected data name.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-11 18:35:36 +0900<br />
Author date: 2012-06-11 18:35:36 +0900<br />
Commit id: 3e48079cc0d3f747232d6d1ab4dcde79f3fa1e3b<br />
Renamed codon_ids.table.txt to match man/data-codon_ids.Rd.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-11 17:00:19 +0900<br />
Author date: 2012-06-11 17:00:19 +0900<br />
Commit id: 601a7072a32d20e8d3eb5f2ecbf5c2c92c1786f7<br />
ASCII quotes to simplify encoding.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-06-11 16:56:33 +0900<br />
Author date: 2012-06-11 16:56:33 +0900<br />
Commit id: fe9d1e38804a7ac7c52c3bac3a19518fa8acc840<br />
Correct documentation links.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-05-16 16:47:44 +0900<br />
Author date: 2012-05-16 16:47:44 +0900<br />
Commit id: 53b4aa6893a7f1e609fe7c26be703c34ee6ca354<br />
Corrected documentaion example.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-05-16 16:26:40 +0900<br />
Author date: 2012-05-16 16:26:40 +0900<br />
Commit id: ced03a73c0cc4becd4285ff4b673fd8e8b7274d9<br />
Use the provided clonotype table instead of the previously hardcoded one.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-05-16 16:24:53 +0900<br />
Author date: 2012-05-16 16:24:53 +0900<br />
Commit id: 00aed02d14797f986f23c15cf269d4a752f33704<br />
Exit with error if filename is an empty string.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-05-16 16:18:18 +0900<br />
Author date: 2012-05-16 16:18:18 +0900<br />
Commit id: f120a81e0fd88beb3d4c408db9841c3a3c0cb9b8<br />
Dedicate to public domain (to be confirmed by public release).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-05-16 16:05:15 +0900<br />
Author date: 2012-05-16 16:05:15 +0900<br />
Commit id: 73621a30be2c8c23a10fafb2ec19979851106b75<br />
Corrected markup syntax errors.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-05-16 15:47:51 +0900<br />
Author date: 2012-05-16 15:47:51 +0900<br />
Commit id: 00ac560dbc024b2e958367e3ce5805df40193767<br />
Correction of how to load example data.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-04-24 20:44:21 +0900<br />
Author date: 2012-04-24 20:44:21 +0900<br />
Commit id: 8afb7daf712b6af1c787aa69fa66d17f0b7b028f<br />
Syntax correction.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-04-24 20:41:34 +0900<br />
Author date: 2012-04-24 20:41:34 +0900<br />
Commit id: c1913a3da561be08528be6372365343a6c0a6efe<br />
Syntax corrections.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-04-24 20:18:33 +0900<br />
Author date: 2012-04-24 20:18:33 +0900<br />
Commit id: 99c3c73fea6e5cb8b4eea47dfb021bb729339b8a<br />
Do more regression tests.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-04-24 20:18:00 +0900<br />
Author date: 2012-04-24 20:18:00 +0900<br />
Commit id: 357f8c5faa6d4ac7c6ebe3c60ee2e0f5f68930dd<br />
Abort if no "improductive" column is found.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-04-24 20:17:27 +0900<br />
Author date: 2012-04-24 20:17:27 +0900<br />
Commit id: 105b91829fec2ead2a6988b8e845e7fa9732142a<br />
Corrected to also accept the OSCT format.<br />
Order Switchable Column Table (OSCT): http://sourceforge.net/projects/osctf/<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-04-05 21:15:17 +0900<br />
Author date: 2012-04-05 21:15:17 +0900<br />
Commit id: 85c55309a1a390a84dc7c9b57e304e62ef869502<br />
Closes example section.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-30 19:40:56 +0900<br />
Author date: 2012-03-30 19:40:56 +0900<br />
Commit id: 743444726e12ea782c6ca3d018bb3f324b138f14<br />
Re-indexed using BWA 0.6.1-r104.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-28 15:41:31 +0900<br />
Author date: 2012-03-28 15:41:31 +0900<br />
Commit id: c2fc8bfd29f3d2819734c57db907a62cf19e173d<br />
Default directories for extraction.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-14 20:09:45 +0900<br />
Author date: 2012-03-14 20:09:45 +0900<br />
Commit id: bfbc7d135702a3f59ac8ac53c5b5047f6f71de08<br />
Tweaks to allow exection from any directory.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-01 19:27:53 +0900<br />
Author date: 2012-03-01 19:27:53 +0900<br />
Commit id: acf2ca9cae299fed66c4175785f00cbe6eb1a59e<br />
clontyperR {convert|detect|extract}<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-01 15:12:18 +0900<br />
Author date: 2012-03-01 15:12:18 +0900<br />
Commit id: dbd6825403c669a58f8ddfff892d404a35c1d955<br />
Removed suffix.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-01 15:03:56 +0900<br />
Author date: 2012-03-01 15:03:56 +0900<br />
Commit id: 86929836cbbc33a4a28451aa7fcf0b7786117886<br />
Added a “clean” target.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-03-01 14:56:08 +0900<br />
Author date: 2012-03-01 14:56:08 +0900<br />
Commit id: 32f65255e3b94257c273bfb956e81d8f0e37a60d<br />
Polishing.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-02-08 17:56:39 +0900<br />
Author date: 2012-02-08 17:56:39 +0900<br />
Commit id: 014a9447214b8f40f53b5352b9f9a55dfcd6e02f<br />
Polishing documentation.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-02-08 16:38:28 +0900<br />
Author date: 2012-02-08 16:38:28 +0900<br />
Commit id: 6a7b0d1672f7c0f5541c51edee914434e52bf3b0<br />
Typography.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-02-08 16:06:23 +0900<br />
Author date: 2012-02-08 16:06:23 +0900<br />
Commit id: 2d1373fc10063873145b5c5f0f3ee27905bf9d6f<br />
Added a “all” target.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-02-08 15:46:09 +0900<br />
Author date: 2012-02-08 15:46:09 +0900<br />
Commit id: 0e4a5040ec2a720a9f40e947decb37b39a1a6288<br />
Need more example data.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-02-08 15:45:35 +0900<br />
Author date: 2012-02-08 15:45:35 +0900<br />
Commit id: 446bc0f82175623f9757384e7b08478b3813b3da<br />
Added URL to BioPerl.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-02-08 15:38:19 +0900<br />
Author date: 2012-02-08 15:38:19 +0900<br />
Commit id: d063e96963be169fa08c864ae34f0e28048b4ee6<br />
Rough implementation with codon IDs. Needs triplechecking.<br />
V and J segment names need to be corrected.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-01-31 21:50:46 +0900<br />
Author date: 2012-01-31 21:50:46 +0900<br />
Commit id: 54db3f0b0b5aa0cf85bdecc1510c42e81c5ba5cc<br />
Documented what the code is doing.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-01-31 20:59:16 +0900<br />
Author date: 2012-01-31 20:59:16 +0900<br />
Commit id: b146a6e49da766c2e1e12cde68e7d5ea7b2f0b24<br />
Attempt at pre-loading J_before_FGxG and V_after_C.<br />
This will probably not work du permier coup.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-01-31 20:49:31 +0900<br />
Author date: 2012-01-31 20:49:31 +0900<br />
Commit id: 33f349b81daf0a93522947ec322817870cdbe495<br />
Replace NA per FALSE; is.somatic is used in a while loop.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-01-30 22:03:28 +0900<br />
Author date: 2012-01-30 22:03:28 +0900<br />
Commit id: aea439fafba06808caa7e4c63e52a9aaf88c2dbe<br />
First step to implement Yassai's nomenclature: the CDR3.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-01-30 21:27:56 +0900<br />
Author date: 2012-01-30 21:27:56 +0900<br />
Commit id: bca53f58171a8531527c27ba95dce30ec612d9bf<br />
Added codon ID table for the Yassai nomenclature.<br />
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706371/table/Tab1/<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2012-01-30 16:12:14 +0900<br />
Author date: 2012-01-30 16:12:14 +0900<br />
Commit id: b4719e4cb8ec41af182655dfcbfdbefd6168b63d<br />
Preparing the use of the OSCTable format.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-12-08 13:16:07 +0900<br />
Author date: 2011-12-08 13:16:07 +0900<br />
Commit id: efd107dea8443a28cc323499ad8817a3930168ae<br />
Draft instructions and script to extract clonotypes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-17 16:03:45 +0900<br />
Author date: 2011-11-17 16:03:45 +0900<br />
Commit id: 9d7dbca10624f2c17aeecd66c27012ef786f133d<br />
Standardised options, shortened error messages, added one check.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-16 20:20:20 +0900<br />
Author date: 2011-11-16 19:33:21 +0900<br />
Commit id: c550e00f807a29c1289df2c295315696f127a880<br />
Reordered options in clonotype.table, and corrected for single libraries.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-16 18:50:18 +0900<br />
Author date: 2011-11-16 18:50:18 +0900<br />
Commit id: df93f52d317c28460043b0eb3e3dc58c369c843b<br />
A function to list unique clonotypes.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-14 16:36:16 +0900<br />
Author date: 2011-11-14 16:36:16 +0900<br />
Commit id: fac03e7856569142cda91dc03634ba8e25f006ad<br />
New function to prepare clonotype tables.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-08 22:09:24 +0900<br />
Author date: 2011-11-08 22:09:24 +0900<br />
Commit id: eaf026e1561dffb78d2de39fc512c43464d966f9<br />
Test data using three libraries.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-08 22:08:24 +0900<br />
Author date: 2011-11-08 22:08:24 +0900<br />
Commit id: c9ba9d9961824143a0377da909715ec84a5ab71c<br />
Integrate the calculation of the eight column: improductive rearrangements.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-08 21:26:40 +0900<br />
Author date: 2011-11-08 21:26:40 +0900<br />
Commit id: d51893483065123767653044ff73a714d10aa685<br />
Function “read.clonotypes” to load a clonotypes file, and example data.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-11-04 22:17:34 +0900<br />
Author date: 2011-11-04 22:06:06 +0900<br />
Commit id: adb605e8a90ec5639d854a91e994a57a5684e794<br />
BWA index of trimmed V segments.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-10-31 14:47:00 +0900<br />
Author date: 2011-10-31 14:47:00 +0900<br />
Commit id: 30576e3dc2856f96a67a7dc5226df8a2a0810824<br />
Reference V and J segments trimmed at C or FGxG motifs.<br />
Needed for V-J extraction by the “VJsplit” script.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-10-31 14:27:37 +0900<br />
Author date: 2011-10-31 14:27:37 +0900<br />
Commit id: 8c2f82eda0e73ad7f4f77bebc72e5cea04c3a9d3<br />
Reference V and J alignment (made by hand using SeaView).<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-10-31 14:27:16 +0900<br />
Author date: 2011-10-31 14:24:21 +0900<br />
Commit id: 700b879cd76980cf45ab9dfdfdfc242551608fc7<br />
Extraction of the V, (D), J and C segments from the reference sequences.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-10-31 14:23:42 +0900<br />
Author date: 2011-10-31 14:05:23 +0900<br />
Commit id: 1363b60e26074401ff9cf1f2b62e2ecd44217ac1<br />
Added reference TCR genes from RefSeq, but BCRs and update helper are needed.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-10-31 12:13:35 +0900<br />
Author date: 2011-10-31 12:13:35 +0900<br />
Commit id: dc77dc1264965d79f786f355f1e91e987132de3d<br />
Initial empty master branch.<br />
Committed by: Charles Plessy<br />
Author Name: Charles Plessy<br />
Commit date: 2011-10-31 12:13:00 +0900<br />
Author date: 2011-10-31 12:13:00 +0900<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@94506 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs.mdwn b/Bugs.mdwn
new file mode 100644
index 0000000..1106591
--- /dev/null
+++ b/Bugs.mdwn
@@ -0,0 +1,12 @@
+If you've found a bug in clonotypeR, post about it here. [[TODO]] items go
+elsewhere. Link items to [[Bugs/done]] when done.
+
+The [[!shortcut name=commit url="http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s"]].
+You can use it to link to the commit that fixed the bug, as in `\[[!commit 7cf11805d84ff8dc6a537c17e73efa275077915d]]`.
+
+There are [[!pagecount pages="Bugs/* and !Bugs/done and !Bugs/discussion and
+!link(patch) and !link(Bugs/done) and !Bugs/*/*"]] "open" bugs:
+
+[[!inline pages="Bugs/* and !Bugs/done and !Bugs/discussion and
+!link(patch) and !link(Bugs/done) and !Bugs/*/*"
+actions=yes rootpage="Bugs" postformtext="Add a new bug titled:" show=0]]
diff --git a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
new file mode 100644
index 0000000..7cdfc91
--- /dev/null
+++ b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
@@ -0,0 +1,55 @@
+Problem
+-------
+
+<pre>
+yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
+# takes ages
+
+yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAGCAACCGCAACTTCAAGTGGCCAGAAGCTGGTT", pep="AATATSSGQKLV"))
+## [1] "aTa.2A14N3A16L12"
+# returns immediately.
+</pre>
+
+
+Troubleshooting
+---------------
+
+The problematic clonotype comes from read `GWYEMNS10GHZUF`.
+
+<pre>
+&#64;GWYEMNS10GHZUF
+gactAACTGGTACACAGCAGGTTCTGGGTTCTGGATGTGCAGGTACACCTTTAATATGGTCCCCTGGCCAAAAACCAGCTTCTGGCCACTTGAAGTTGCACAGAAGTAGGTGGCTGAGTCTCCAGGCTGAGAGTCTTTGATGTGCAAGGAGAGATTTTTCTCCCTTTTATTGAAGAAGATTGTGAATCGTCCATCTTCCTTTTTATCGGACACTGAACGTATGGCTATCAGGAGAGCAGGGCCTTCCCCAGGGAACTGCTGGTACCATGGGAAGTAGTCAAAAGCACTGTTCTCAtaactagcagttcagaattgcggtctctccttccccagactgtcagagattggagtcgtgggagacaaggcacacaggggataggngngnnnnnnnnnnnnn
++
+FFF::;;FFFFFFFFIIIIHFFFHF666=&lt;FFGGDDDFFHFDIIIIIIIHHHIIIHFFFD54449662200001335&gt;&gt;AAABDFDDDFDDDFFFFFFFFFFFFFFFFFCCCCCFFFFFFFFFFFFDDBBBBB==110?&#64;&#64;&#64;&#64;&#64;&gt;4455BBA??3357;F4:::;;==D88?AA&lt;;:==BAAAA==??AAB&#64;AAA=&gt;&gt;&gt;222//02A8898BDDFFFDDFFFFFF666:DBAAAABB:::???DD;;;;D?????DDBA?&lt;&lt;&lt;&gt;&lt;&lt;&lt;&lt;000444&lt;8993222233393...:663322&lt;9233776899:;;963326755551111,,,,3313335333799.....23322666726;;;66772222,,,,47400!,!,!!!!!!!!!!!!!
+</pre>
+
+Here is the alignment made by clonotypeR
+
+<pre>
+GWYEMNS10GHZUF 16 TRAV14N-3 105 17 49S17M1I29M1I201M99S * 0 0 NNNNNNNNNNNNNCNCNCCTATCCCCTGTGTGCCTTGTCTCCCACGACTCCAATCTCTGACAGTCTGGGGAAGGAGAGACCGCAATTCTGAACTGCTAGTTATGAGAACAGTGCTTTTGACTACTTCCCATGGTACCAGCAGTTCCCTGGGGAAGGCCCTGCTCTCCTGATAGCCATACGTTCAGTGTCCGATAAAAAGGAAGATGGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAATCTCTCCTTGCACATCAAAGACTCTCAGCCTGGAGACTCAGCCACCTACTTCTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATATTAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTAGTC !!!!!!!!!!!!!,!,!00474,,,,22227766;;;62766622332.....9973335333133,,,,111155557623369;;:9986773329&lt;223366:...3933322223998&lt;444000&lt;&lt;&lt;&lt;&gt;&lt;&lt;&lt;?ABDD?????D;;;;DD???:::BBAAAABD:666FFFFFFDDFFFDDB8988A20//222&gt;&gt;&gt;=AAA&#64;BAA??==AAAAB==:;&lt;AA?88D==;;:::4F;7533??ABB5544&gt;&#64;&#64;&#64;&#64;&#64;?011==BBBBBDDFFFFFFFFFFFFCCCCCFFFFFFFFFFFFFFFFFDDDFDDDFDBAAA&gt;&gt;53310000226694445DFFFHIIIHHHIIIIIIIDFHFFDDDGGFF&lt;=666FHFFFHIIIIFFFFFFFF;;::FFF AS:i:233 XS:i:218 XF:i:3 XE:i:4 XN:i:0
+</pre>
+
+The problem was that the V segment was completely digested in favor of the J segment.
+
+<pre>
+ 351 400
+GWYEMNS10GHZUF CTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
+TRAJ16 ~~~~GCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
+TRAV14N-3 CTGTGCAGC...AAGTG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ 401 450
+GWYEMNS10GHZUF TAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTA
+TRAJ16 TAAAGGTGTACCTGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+TRAV14N-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+</pre>
+
+This triggered an infinite loop when calling `is.germline()`.
+
+[[Done]] in `42ab98729c5c77462b5929b00ee973074ae4c1c7`.
+
+Now the function should return as in the following example.
+
+<pre>
+yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
+## [1] "a.A14N3A16L9"
+</pre>
diff --git a/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn b/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
new file mode 100644
index 0000000..a4efb15
--- /dev/null
+++ b/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
@@ -0,0 +1,31 @@
+Is it a bug in the software or a bug in the concept ?
+
+<pre>
+> rownames(dd)[grep('aAn.1A14-1A43L9', dd.yassai)]
+[1] "TRAV14-1 TRAJ43 GCAGCAGCTAACAACAATGCCCCACGA AAANNNAPR"
+[2] "TRAV14-1 TRAJ43 GCAGCTAATAACAACAATGCCCCACGA AANNNNAPR"
+> V_after_C['TRAV14-1',]
+[1] "GCAGCAAGTG"
+> J_before_FGxG['TRAJ43',]
+[1] "GCAATAACAACAATGCCCCACGA"
+</pre>
+
+<pre>
+aAn.1A14-1A43L9
+ A A A N N N A P R
+GCA GCA GCT AAC AAC AAT GCC CCA CGA
+GCA GCA agt g
+ gc aaT AAC AAC AAT GCC CCA CGA
+</pre>
+
+<pre>
+aAn.1A14-1A43L9
+ A A N N N N A P R
+GCA GCT AAT AAC AAC AAT GCC CCA CGA
+GCA GCa agt g
+ gc AAT AAC AAC AAT GCC CCA CGA
+</pre>
+
+----
+
+This is a collision (different colonotypes giving the same Yassai ID) rather than a bug in the implementation → [[done]].
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
new file mode 100644
index 0000000..c95cbe8
--- /dev/null
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -0,0 +1,18 @@
+The reason is the following bug in EMBOSS.
+
+<pre>
+echo -e '>A\nAAAAAA' > test-1.fa
+cat test-1.fa
+# >A
+# AAAAAA
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# >A
+# AAAAAA
+mkdir test
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
+# Error: Unable to read sequence 'test-1.fa:A'
+# Died: seqret terminated: Bad value for '-sequence' and no prompt
+</pre>
diff --git a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
new file mode 100644
index 0000000..1648dce
--- /dev/null
+++ b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
@@ -0,0 +1,13 @@
+<pre>
+> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
+[1] "tg.integer(0)A2A61L13"
+</pre>
+
+[[Done]] in `2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd`, by return an empty chain instead of `integer(0)` when receiving an empty chain.
+
+Result after correction:
+
+<pre>
+> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
+[1] "tg.A2A61L13"
+</pre>
diff --git a/Bugs/Use_basename_case-insensitively.mdwn b/Bugs/Use_basename_case-insensitively.mdwn
new file mode 100644
index 0000000..95a3173
--- /dev/null
+++ b/Bugs/Use_basename_case-insensitively.mdwn
@@ -0,0 +1,6 @@
+Problem:
+
+ $ basename foo.fastq .fastq
+ foo
+ $ basename foo.FASTQ .fastq
+ foo.FASTQ
diff --git a/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn b/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
new file mode 100644
index 0000000..3899e4e
--- /dev/null
+++ b/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
@@ -0,0 +1,18 @@
+This would prevent horrors like:
+
+<pre>
+$ ../scripts/clonotypeR detect .fastq
+[bam_header_read] EOF marker is absent. The input is probably truncated.
+[bsw2_aln] fail to open file '.fastq'. Abort!
+[samopen] SAM header is present: 169 sequences.
+[sam_read1] reference 'SN:TRDV5 LN:344
+3
+
+19
+
+3
+
+
+' is recognized as '*'.
+[main_samview] truncated file.
+</pre>
diff --git a/Bugs/done.mdwn b/Bugs/done.mdwn
new file mode 100644
index 0000000..0a666ab
--- /dev/null
+++ b/Bugs/done.mdwn
(Diff truncated)
</pre>
</div>
change to DESCRIPTION NAMESPACE on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_e2388f68d34bcb0b1d72475237341782eed2479c/
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2014-09-25T02:27:33Z
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Explicitely import setMethod in NAMESPACE.<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index c73ec16..8e69f9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: High throughput analysis of T cell antigen receptor sequences
The purpose of this package is to process and quantitatively analyse millions
of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
License: file LICENSE
-Depends: methods
+Imports: methods
Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
VignetteBuilder: knitr
Packaged: 2013-12-11 10:22:39 UTC; charles
diff --git a/NAMESPACE b/NAMESPACE
index d75f824..2d083c2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,2 @@
+importFrom(methods, setMethod)
exportPattern("^[[:alpha:]]+")
</pre>
</div>
change to DESCRIPTION vignettes/clonotypeR.Rmd on clonotypeR
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</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index a0daca5..c73ec16 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.1.6
+Version: 1.3.1
Date: 2014-04-08
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index f121ece..3de0e56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -39,7 +39,7 @@ examples are available on line at
*This example analysis assumes a
[unix](https://en.wikipedia.org/wiki/Operating%5Fsystem%23UNIX%5Fand%5FUNIX%2Dlike%5Foperating%5Fsystems)
-system (Linux, Mac OS, …)*
+system (Linux, Mac OS, ...)*
Test data
@@ -105,11 +105,11 @@ or to calculate distance between libraries, for instance with the
`vegan` package.
-Example data (3 × 2,000 reads)
+Example data (3 x 2,000 reads)
------------------------------
The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors α (2,000
+is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
reads each) made on the 454 Titanium or the 454 junior platforms. The original
libraries will be deposited in public databanks after publication in a
peer-reviewed journal.
</pre>
</div>
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2014-06-05T10:40:12Z
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<pre>
diff --git a/index.mdwn b/index.mdwn
index 7a89d51..357e7b9 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -45,6 +45,8 @@ to try alternative solutions, you can have a look at
### Recent news
+ * March 2014: New stable version [1.2](http://www.bioconductor.org/packages/2.14/bioc/html/clonotypeR.html)
+ released on Bioconductor.
* 11 December 2013: Version 1.1.3 adding a `long` option to `yassai_identifier`, solving
the problem of ID collisions.
* 23 October 2013: Version 1.1.2 adding a new option to `clonotype_table` for randomly
</pre>
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change to Bugs/Does_not_work_with_EMBOSS_6.6.0. on clonotypeR
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<span class="desc"><br />Changed pages:</span>
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn;h=c95cbe81b47eeca68d2d67c6eee610dce2ea9363;hp=0000000000000000000000000000000000000000;hb=67aa2eac309df5bf8d5dbc790661db102145d692;hpb=fe4ae4f131d3c5fc8d5aebd5873d7de109c1b0b7" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FDoes_not_work_with_EMBOSS_6.6.0.&do=goto" rel="nofollow">Bugs/Does not work with EMBOSS 6.6.0.</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-06-05T05:22:35Z" class="relativedate" title="Thu, 05 Jun 2014 05:22:35 +0000">05:22:35 06/05/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Does not work with EMBOS 6.6.0.<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
new file mode 100644
index 0000000..c95cbe8
--- /dev/null
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -0,0 +1,18 @@
+The reason is the following bug in EMBOSS.
+
+<pre>
+echo -e '>A\nAAAAAA' > test-1.fa
+cat test-1.fa
+# >A
+# AAAAAA
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# >A
+# AAAAAA
+mkdir test
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
+# Error: Unable to read sequence 'test-1.fa:A'
+# Died: seqret terminated: Bad value for '-sequence' and no prompt
+</pre>
</pre>
</div>
change to Bugs/Use_basename_case-insensitively on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_fe4ae4f131d3c5fc8d5aebd5873d7de109c1b0b7/
https://launchpad.net/~plessy
2014-06-04T22:38:29Z
2014-06-04T22:38:29Z
<div id="change-fe4ae4f131d3c5fc8d5aebd5873d7de109c1b0b7" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=Bugs/Use_basename_case-insensitively.mdwn;h=95a3173f43bb3836ee4a4c91e28b3040ab469469;hp=0000000000000000000000000000000000000000;hb=fe4ae4f131d3c5fc8d5aebd5873d7de109c1b0b7;hpb=517e35af4a8ad194bed6ea3d187c73e5b97490b7" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?page=Bugs%2FUse_basename_case-insensitively&do=goto" rel="nofollow">Bugs/Use basename case-insensitively</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="https://launchpad.net/~plessy" rel="nofollow">plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">web</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-06-04T22:38:29Z" class="relativedate" title="Wed, 04 Jun 2014 22:38:29 +0000">22:38:29 06/04/14</time></span>
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</span>
</div>
<div class="changelog">
Should use `basename` canse-insensitively…<br />
</div>
<div class="diff">
<pre>
diff --git a/Bugs/Use_basename_case-insensitively.mdwn b/Bugs/Use_basename_case-insensitively.mdwn
new file mode 100644
index 0000000..95a3173
--- /dev/null
+++ b/Bugs/Use_basename_case-insensitively.mdwn
@@ -0,0 +1,6 @@
+Problem:
+
+ $ basename foo.fastq .fastq
+ foo
+ $ basename foo.FASTQ .fastq
+ foo.FASTQ
</pre>
</div>
change to DESCRIPTION vignettes/clonotypeR.Rmd on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_431538c61f3167a3e9b78565bc744eba0258ed81/
d.tenenbaum
2014-05-27T22:15:24Z
2014-05-27T22:15:24Z
<div id="change-431538c61f3167a3e9b78565bc744eba0258ed81" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=c73ec16d7b7ff5c1420b5b490c9ebf24075af386;hp=1309b59b17c3db3c2ed1d87e7a03fc36b778cfc3;hb=431538c61f3167a3e9b78565bc744eba0258ed81;hpb=4e977f5cbde8b8173fd27c7820073197e76a764d" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=vignettes/clonotypeR.Rmd;h=3de0e56c2c6ec0911b9ac35b7dc459fbf99ab5bc;hp=f121ece2c8afb34ddffdb161b8bee27488ae8c4b;hb=431538c61f3167a3e9b78565bc744eba0258ed81;hpb=4e977f5cbde8b8173fd27c7820073197e76a764d" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=vignettes%2FclonotypeR.Rmd" rel="nofollow">vignettes/clonotypeR.Rmd</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=d.tenenbaum" rel="nofollow">d.tenenbaum</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-05-27T22:15:24Z" class="relativedate" title="Tue, 27 May 2014 22:15:24 +0000">22:15:24 05/27/14</time></span>
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</span>
</div>
<div class="changelog">
replace non-ascii characters in vignette so build does not time out on Mavericks<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@90751 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 1309b59..c73ec16 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.0
+Version: 1.3.1
Date: 2014-04-08
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index f121ece..3de0e56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -39,7 +39,7 @@ examples are available on line at
*This example analysis assumes a
[unix](https://en.wikipedia.org/wiki/Operating%5Fsystem%23UNIX%5Fand%5FUNIX%2Dlike%5Foperating%5Fsystems)
-system (Linux, Mac OS, …)*
+system (Linux, Mac OS, ...)*
Test data
@@ -105,11 +105,11 @@ or to calculate distance between libraries, for instance with the
`vegan` package.
-Example data (3 × 2,000 reads)
+Example data (3 x 2,000 reads)
------------------------------
The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors α (2,000
+is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
reads each) made on the 454 Titanium or the 454 junior platforms. The original
libraries will be deposited in public databanks after publication in a
peer-reviewed journal.
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_4e977f5cbde8b8173fd27c7820073197e76a764d/
d.tenenbaum
2014-04-11T21:21:21Z
2014-04-11T21:21:21Z
<div id="change-4e977f5cbde8b8173fd27c7820073197e76a764d" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=1309b59b17c3db3c2ed1d87e7a03fc36b778cfc3;hp=1b4302bb87075fed37b466a5a1e50a405b150ac7;hb=4e977f5cbde8b8173fd27c7820073197e76a764d;hpb=458f93f5124c5a2165ccb652febdf4c05297e007" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=d.tenenbaum" rel="nofollow">d.tenenbaum</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-04-11T21:21:21Z" class="relativedate" title="Fri, 11 Apr 2014 21:21:21 +0000">21:21:21 04/11/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
Second version bump after creating 2.14 release branch.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@88840 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index 1b4302b..1309b59 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.2.0
+Version: 1.3.0
Date: 2014-04-08
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to DESCRIPTION on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_458f93f5124c5a2165ccb652febdf4c05297e007/
d.tenenbaum
2014-04-11T21:07:21Z
2014-04-11T21:07:21Z
<div id="change-458f93f5124c5a2165ccb652febdf4c05297e007" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=DESCRIPTION;h=1b4302bb87075fed37b466a5a1e50a405b150ac7;hp=a0daca5e9721a9929c4c526f4ff56f783e5d6d5b;hb=458f93f5124c5a2165ccb652febdf4c05297e007;hpb=577b609e43c48206151255a7876e584c94aeaf90" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=DESCRIPTION" rel="nofollow">DESCRIPTION</a>
</span>
<span class="desc"><br />Changed by:</span>
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<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=d.tenenbaum" rel="nofollow">d.tenenbaum</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-04-11T21:07:21Z" class="relativedate" title="Fri, 11 Apr 2014 21:07:21 +0000">21:07:21 04/11/14</time></span>
<span class="desc"><br /></span>
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</span>
</div>
<div class="changelog">
First version bump prior to creating 2.14 branch.<br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@88838 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/DESCRIPTION b/DESCRIPTION
index a0daca5..1b4302b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.1.6
+Version: 1.2.0
Date: 2014-04-08
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
</pre>
</div>
change to ChangeLog on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_577b609e43c48206151255a7876e584c94aeaf90/
c.plessy
2014-04-09T03:44:24Z
2014-04-09T03:44:24Z
<div id="change-577b609e43c48206151255a7876e584c94aeaf90" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=ChangeLog;h=8c90a5285d663a45d860a0f9e6013d46b84ea6c8;hp=96b84e2618a3a8982849931f574c7efebbf8a0a8;hb=577b609e43c48206151255a7876e584c94aeaf90;hpb=e23ced41f80de3559fed2a0e9da225ef359ebb7d" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=ChangeLog" rel="nofollow">ChangeLog</a>
</span>
<span class="desc"><br />Changed by:</span>
<span class="committer">
<a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=c.plessy" rel="nofollow">c.plessy</a>
</span>
<span class="desc"><br />Commit type:</span>
<span class="committype">git</span>
<span class="desc"><br />Date:</span>
<span class="changedate"><time datetime="2014-04-09T03:44:24Z" class="relativedate" title="Wed, 09 Apr 2014 03:44:24 +0000">03:44:24 04/09/14</time></span>
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</span>
</div>
<div class="changelog">
Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 1 commit(s).<br />
Commit information:<br />
Commit id: d1cde58657ad1aac7125dbffc4c9d7b7a500236d<br />
Commit message:<br />
Spellchecked ChangeLog.<br />
The goal is to test the commit hook…<br />
Committed by Charles Plessy <plessy at riken.jp><br />
Commit date: 2014-04-09T12:43:28+09:00<br />
From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org><br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@88640 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
</div>
<div class="diff">
<pre>
diff --git a/ChangeLog b/ChangeLog
index 96b84e2..8c90a52 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -11,7 +11,7 @@
* Change biocviews to “Sequencing”,
2013-12-11 Charles Plessy <plessy@riken>
- * Commited 1.1.3 to Bioconductor.
+ * Committed 1.1.3 to Bioconductor.
* Fixed two bugs in yassai_identifier().
- Infinite loop when the CDR3 is fully contained in the J segment.
- Bogus 'integer(0)' output when there are only germline residues.
</pre>
</div>
change to ChangeLog DESCRIPTION NEWS on clonotypeR
http://clonotyper.branchable.com/recentchanges/change_e23ced41f80de3559fed2a0e9da225ef359ebb7d/
c.plessy
2014-04-09T03:44:19Z
2014-04-09T03:44:19Z
<div id="change-e23ced41f80de3559fed2a0e9da225ef359ebb7d" class="metadata">
<span class="desc"><br />Changed pages:</span>
<span class="pagelinks">
<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=ChangeLog;h=96b84e2618a3a8982849931f574c7efebbf8a0a8;hp=0000000000000000000000000000000000000000;hb=e23ced41f80de3559fed2a0e9da225ef359ebb7d;hpb=7abdab7d08c8f7b8ecd1f658bc393f826885ef06" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=ChangeLog" rel="nofollow">ChangeLog</a>
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<a href="http://source.clonotyper.branchable.com/?p=source.git;a=blobdiff;f=NEWS;h=e8067a7c2b7ab58bca1c6c0c3292bcb6106f1211;hp=f3e6131b39d892dc69a9f782f0ef67c3cf930e9b;hb=e23ced41f80de3559fed2a0e9da225ef359ebb7d;hpb=7abdab7d08c8f7b8ecd1f658bc393f826885ef06" title="diff" rel="nofollow"><img src="http://clonotyper.branchable.com/wikiicons/diff.png" alt="diff" /></a><a href="http://clonotyper.branchable.com/ikiwiki.cgi?do=goto&page=NEWS" rel="nofollow">NEWS</a>
</span>
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</span>
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Commit made by the Bioconductor Git-SVN bridge.<br />
Consists of 4 commit(s).<br />
Commit information:<br />
Commit id: c96f345271782e2a274912f2ae6e88097541f56c<br />
Commit message:<br />
Renamed the NEWS file “ChangeLog”, according to its contents.<br />
Committed by Charles Plessy <plessy at riken.jp><br />
Commit date: 2014-04-08T09:33:36+09:00<br />
Commit id: 4a67d1221f27e9fdcb7af0ef0dd27abfb5c8c46c<br />
Commit message:<br />
Synthethic release notes to be used with utils::news() in R.<br />
Committed by Charles Plessy <plessy at riken.jp><br />
Commit date: 2014-04-08T09:51:21+09:00<br />
Commit id: e1791c38aaeca01f11082d0afef37c5cd6defacc<br />
Commit message:<br />
Repair DESCRIPTION file.<br />
Committed by Charles Plessy <plessy at riken.jp><br />
Commit date: 2014-04-08T15:43:09+09:00<br />
Commit id: a8aa49a05e10bc943a44fa3809766a88c9a2fa8d<br />
Commit message:<br />
Version 1.1.6.<br />
Committed by Charles Plessy <plessy at riken.jp><br />
Commit date: 2014-04-08T15:44:25+09:00<br />
From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org><br />
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clonotypeR@88639 bc3139a8-67e5-0310-9ffc-ced21a209358<br />
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diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..96b84e2
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,80 @@
+2014-04-08 Charles Plessy <plessy@riken.jp>
+ * Version 1.1.6
+ * Transfer “NEWS” to ChangeLog and add release notes to “NEWS”.
+
+2014-04-03 Charles Plessy <plessy@riken.jp>
+ * Version 1.1.5
+ * Mention the GitHub bridge in the documentation
+
+2014-03-05 Bioc admins
+ * Version 1.1.4.
+ * Change biocviews to “Sequencing”,
+
+2013-12-11 Charles Plessy <plessy@riken>
+ * Commited 1.1.3 to Bioconductor.
+ * Fixed two bugs in yassai_identifier().
+ - Infinite loop when the CDR3 is fully contained in the J segment.
+ - Bogus 'integer(0)' output when there are only germline residues.
+ * Avoid more collisions by indicating the position of the V-J junction
+ when there is no codon ID to indicate.
+ * Mark and filter out clonotypes with ambiguous ('N') nucleotides.
+
+2013-12-05 Charles Plessy <plessy@riken>
+ * New "long" option to yassai_identifier(), to avoid collisions.
+
+2013-11-19 Charles Plessy <plessy@riken.jp>
+ * New references from NCBI, updating TRDV5.
+
+2013-10-23 Charles Plessy <plessy@riken.jp>
+ * Commited 1.1.2 to Bioconductor.
+ * clonotype_table: new option to randomly "sample" libraries.
+
+2013-10-17 Charles Plessy <plessy@riken.jp>
+ * Commited 1.1.1 to Bioconductor.
+ * common_clonotypes: new mode to calculate the "abundance" relatively
+ to one library.
+
+2013-10-07 Charles Plessy <plessy@riken.jp>
+ * Commited 0.99.6 to Bioconductor.
+ * Added unit tests for yassai_identifier().
+
+2013-08-01 Charles Plessy <plessy@riken.jp>
+ * Unified the syntax of common_clonotypes and unique_clonotypes.
+
+2013-05-07 Charles Plessy <plessy@riken.jp>
+ * Resubmitted 0.99.5 to Bioconductor.
+ * Distribute a copy of the clonotypes extracted from example_data.
+ * Execute all examples in the vignette.
+
+2013-05-01 Charles Plessy <plessy@riken.jp>
+
+ * Resubmitted 0.99.4 to Bioconductor
+ * Moved the Markdown vignette to '/vignettes'.
+ * Added executable example with test data to the vignette.
+
+2013-04-26 Charles Plessy <plessy@riken.jp>
+
+ * Resubmitted 0.99.3 to Bioconductor
+ * Moved extra data to 'inst/extdata'.
+ * Moved the Markdown vignette to 'inst/vignettes'.
+
+2013-04-15 Charles Plessy <plessy@riken.jp>
+
+ * Resubmission after correcting yassai_identifier() and other warnings.
+
+2013-01-08 Charles Plessy <plessy@riken.jp>
+
+ * Leaner Bioconductor package, without the wiki documentation.
+
+2012-..... Charles Plessy <plessy@riken.jp>
+
+ * Many entries missing.
+
+2012-10-10 Charles Plessy <plessy@riken.jp>
+
+ * Corrected Frenglish “improductive” with “unproductive”.
+ This can break backwards compatibility.
+
+2012-09-06 Charles Plessy <plessy@riken.jp>
+
+ * Initial release
diff --git a/DESCRIPTION b/DESCRIPTION
index ee152f8..a0daca5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,21 +1,19 @@
Package: clonotypeR
Type: Package
Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.1.4
-Date: 2013-12-11
+Version: 1.1.6
+Date: 2014-04-08
Author: Charles Plessy <plessy@riken.jp>
Maintainer: Charles Plessy <plessy@riken.jp>
-Description: High throughput analysis of T cell antigen receptor
- sequences The genes encoding T cell receptors are created by
- somatic recombination, generating an immense combination of V,
- (D) and J segments. Additional processes during the
- recombination create extra sequence diversity between the V an
- J segments. Collectively, this hyper-variable region is called
- the CDR3 loop.
+Description: High throughput analysis of T cell antigen receptor sequences
+ The genes encoding T cell receptors are created by somatic recombination,
+ generating an immense combination of V, (D) and J segments. Additional
+ processes during the recombination create extra sequence diversity between the
+ V an J segments. Collectively, this hyper-variable region is called the CDR3
+ loop.
.
- The purpose of this package is to process and quantitatively analyse
- millions of V-CDR3-J combination, called clonotypes, from
- multiple sequence libraries.
+ The purpose of this package is to process and quantitatively analyse millions
+ of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
License: file LICENSE
Depends: methods
Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
diff --git a/NEWS b/NEWS
index f3e6131..e8067a7 100644
--- a/NEWS
+++ b/NEWS
@@ -1,76 +1,28 @@
-2014-04-03 Charles Plessy <plessy@riken.jp>
- * Version 1.1.5
- * Mention the GitHub bridge in the documentation
+Changes in version 1.2.0
-2014-03-05 Bioc admins
- * Version 1.1.4.
- * Change biocviews to “Sequencing”,
+NEW FEATURES
-2013-12-11 Charles Plessy <plessy@riken>
- * Commited 1.1.3 to Bioconductor.
- * Fixed two bugs in yassai_identifier().
- - Infinite loop when the CDR3 is fully contained in the J segment.
- - Bogus 'integer(0)' output when there are only germline residues.
- * Avoid more collisions by indicating the position of the V-J junction
- when there is no codon ID to indicate.
- * Mark and filter out clonotypes with ambiguous ('N') nucleotides.
+ o Added a “long” option to yassai_identifier(), where every amino acid is
+ represented. This solves the problem of ID collisions, where a single
+ identifier could be produced by two different clonotypes.
-2013-12-05 Charles Plessy <plessy@riken>
- * New "long" option to yassai_identifier(), to avoid collisions.
+ o Added a new option to clonotype_table() for randomly sampling libraries.
-2013-11-19 Charles Plessy <plessy@riken.jp>
- * New references from NCBI, updating TRDV5.
+ o Added a new mode to common_clonotypes() for calculating the abundance
+ relatively to one library.
-2013-10-23 Charles Plessy <plessy@riken.jp>
- * Commited 1.1.2 to Bioconductor.
- * clonotype_table: new option to randomly "sample" libraries.
+ o Unified the syntax of common_clonotypes() and unique_clonotypes().
-2013-10-17 Charles Plessy <plessy@riken.jp>
- * Commited 1.1.1 to Bioconductor.
- * common_clonotypes: new mode to calculate the "abundance" relatively
- to one library.
+BUG FIXES
-2013-10-07 Charles Plessy <plessy@riken.jp>
- * Commited 0.99.6 to Bioconductor.
- * Added unit tests for yassai_identifier().
+ o Removed infinite loop in yassai_identifier() when the germinal V
+ sequence was completely absent from the CDR3.
-2013-08-01 Charles Plessy <plessy@riken.jp>
- * Unified the syntax of common_clonotypes and unique_clonotypes.
+ o Corrected output bug where “integer(0)” was returned if the V–J
+ boundary was a codon boundary.
-2013-05-07 Charles Plessy <plessy@riken.jp>
- * Resubmitted 0.99.5 to Bioconductor.
- * Distribute a copy of the clonotypes extracted from example_data.
- * Execute all examples in the vignette.
+ o yassai_identifier(): properly encode the names of the V and J segments.
-2013-05-01 Charles Plessy <plessy@riken.jp>
+Changes in version 1.0.0
- * Resubmitted 0.99.4 to Bioconductor
- * Moved the Markdown vignette to '/vignettes'.
- * Added executable example with test data to the vignette.
-
-2013-04-26 Charles Plessy <plessy@riken.jp>
-
- * Resubmitted 0.99.3 to Bioconductor
- * Moved extra data to 'inst/extdata'.
- * Moved the Markdown vignette to 'inst/vignettes'.
-
-2013-04-15 Charles Plessy <plessy@riken.jp>
(Diff truncated)
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