期刊
BMC BIOINFORMATICS
卷 16, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s12859-015-0613-1
关键词
Adaptive immunity; T cell receptor; TR repertoire analysis; TR diversity
类别
资金
- MCB program RAS
- RFBR [14-04-01823, 13-04-01124, 14-04-01062, 15-34-21052, MD-3044.2014.4]
- Dynasty Foundation [MK-4583.2015.4]
- [14.604.21.0118]
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.
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