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tcR: an R package for T cell receptor repertoire advanced data analysis
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tcR: an R package for T cell receptor repertoire advanced data analysis
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Journal Article
tcR: an R package for T cell receptor repertoire advanced data analysis
2015
Overview
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.
Publisher
BioMed Central,BioMed Central Ltd
Subject
/ Analysis
/ Biomedical and Life Sciences
/ Computational Biology/Bioinformatics
/ Computer Appl. in Life Sciences
/ High-Throughput Nucleotide Sequencing - methods
/ Humans
/ Receptors, Antigen, T-Cell - genetics
/ Receptors, Antigen, T-Cell - immunology
/ Sequence analysis (Applications)
/ Sequence Analysis, DNA - methods
/ Software
/ T cells
