[HTML][HTML] tcR: an R package for T cell receptor repertoire advanced data analysis

VI Nazarov, MV Pogorelyy, EA Komech, IV Zvyagin… - BMC …, 2015 - Springer
BMC bioinformatics, 2015Springer
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 …
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.
Springer