TcR: an R package for T cell receptor repertoire advanced data analysis. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Nazarov, Vadim; Pogorelyy, Mikhail; Komech, Ekaterina; Zvyagin, Ivan; Bolotin, Dmitry; Shugay, Mikhail; Chudakov, Dmitry; Lebedev, Yury; Mamedov, Ilgar
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 5
• Publication Date: 2015-12
• Subjects: Adaptive immunity -- T cell receptor -- TR repertoire analysis -- TR diversity; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0613-1
• Languages: English
• ISSNs: 1471-2105

Abstract

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.