tcR: an R package for T cell receptor repertoire advanced data analysis |
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Authors: | 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 |
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Institution: | .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 ;.Central European Institute of Technology, Masaryk University, Brno, Czech Republic |
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Abstract: | BackgroundThe 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.ResultsHere 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.ConclusionstcR 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. |
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Keywords: | Adaptive immunity T cell receptor TR repertoire analysis TR diversity |
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