tcR: An R package for T cell receptor repertoire advanced data analysis

Vadim I. Nazarov, Mikhail V. Pogorelyy, Ekaterina A. Komech, Ivan V. Zvyagin, Dmitry A. Bolotin, Mikhail Shugay, Dmitry M. Chudakov, Yury B. Lebedev, Ilgar Z. Mamedov

Research output: Contribution to journalArticlepeer-review

153 Citations (Scopus)

Abstract

Background: The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing. Results: Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies. Conclusions: tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples.

Original languageEnglish
Article number175
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
Publication statusPublished - 12 Dec 2015
Externally publishedYes

Keywords

  • Adaptive immunity
  • T cell receptor
  • TR diversity
  • TR repertoire analysis

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