R package

The R package is also distributed on Bioconductor. It only contains the R code to analyse the clonotypes extracted by the scripts for processing the raw sequences, which are to be downloaded as explained below.

From source repository

Install the requirements below, and then clone clonotypeR with git, then build and install the R module

git clone git:// clonotyper
R CMD build clonotyper
R CMD INSTALL clonotypeR_0.9.tar.gz  # Adjust for the correct version number

See the example analysis of GSE35626 for a more detailed walkthrough.


Run-time requirements

  • EMBOSS, to manipulate the reference sequences.
  • BWA (Burrows-Wheeler Aligner), to identify the trimmed V segments.
  • BioPerl (> 1.6.9), to translate the CDRs. Lower versions differ on how they translate incomplete last codons.
  • R for creating expression tables and analysing them.

Other requirements

  • sff_extract, to convert the 454 SFF files to FASTQ format.
  • Biostrings, to refresh the R tables containging the V and J segment sequence boundaries.
  • Pandoc is needed for building the manual page of clonotypeR.