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

BMC Bioinformatics. 2015 May 28;16(1):175. doi: 10.1186/s12859-015-0613-1.


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 ( ). The source code and development version are available at tcR GitHub ( ) along with the full documentation and typical usage examples.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Immunoglobulins / genetics*
  • Programming Languages
  • Receptors, Antigen, T-Cell / genetics*
  • Receptors, Antigen, T-Cell / immunology*
  • Sequence Analysis, DNA / methods*
  • Software*


  • Immunoglobulins
  • Receptors, Antigen, T-Cell