clonotypeR – Quantitative analysis of antigen receptor sequences

clonotypeR is a Bioconductor package and accompanying scripts to identify and analyse clonotypes from high-throughput T cell receptors sequence libraries. clonotypeR is suited to process and organise very large number of clonotypes, 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.

clonotypeR is developed in the RIKEN Yokohama Campus by the Division for Genomics Technologies of the Center for Life Science Technologies, in collaboration with the Laboratory for Immune Homeostasis of the Center for Integrative Medical Sciences.

• To install clonotypeR, see the instructions.

• To use clonotypeR, see the workflow and the tips.

• To participate to the development: browse the source code, see the TODO and Bugs pages.

We hope that clonotypeR will be useful for you. Please do not hesitate to report bugs or contact Charles Plessy at RIKEN about shortcomings, limitations, or possible developments. If you need to try alternative solutions, you can have a look at IMGTHighV-QUEST, Decombinator, MiTCR, MIGEC, MiXCR, LymAnalyzer, tcR, TraCeR, VDJviz, or VDJtools. See also the OMICtool website for a longer list of repertoire tools.

clonotypeR is placed in the public domain.

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.
• October 2014: New stable version 1.4 released on Bioconductor.
• 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.
• March 2014: New stable version 1.2 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 sampling libraries.
• 17 October 2013: Version 1.1.1 adding a new mode to common_clonotypes for calculating the abundance relatively to one library.
• 1 August 2013: unified the syntax of common_clonotypes and unique_clonotypes.
• 25 May 2013: clonotypeR accepted in Bioconductor

See the NEWS file for a comprehensive list of changes.