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.

Shemyakin Ovchinnikov Institute of Bioorganic Chemistry 16 10 Miklukho Maklaya Moscow 117997 Russia

Shemyakin Ovchinnikov Institute of Bioorganic Chemistry 16 10 Miklukho Maklaya Moscow 117997 Russia Central European Institute of Technology Masaryk University Brno Czech Republic

Shemyakin Ovchinnikov Institute of Bioorganic Chemistry 16 10 Miklukho Maklaya Moscow 117997 Russia National Research University Higher School of Economics 20 Myasnitskaya Ulitsa Moscow 101000 Russia

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