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

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 special...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 16; no. 1; p. 175
Main Authors: Nazarov, Vadim I., Pogorelyy, Mikhail V., Komech, Ekaterina A., Zvyagin, Ivan V., Bolotin, Dmitry A., Shugay, Mikhail, Chudakov, Dmitry M., Lebedev, Yury B., Mamedov, Ilgar Z.
Format: Journal Article
Language:English
Published: London BioMed Central 28.05.2015
BioMed Central Ltd
Subjects:
Algorithms
Analysis
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
High-Throughput Nucleotide Sequencing - methods
Humans
Immune response
Immunoglobulins - genetics
Life Sciences
Microarrays
Physiological aspects
Programming Languages
Receptors, Antigen, T-Cell - genetics
Receptors, Antigen, T-Cell - immunology
Sequence analysis (Applications)
Sequence Analysis, DNA - methods
Software
T cells
TR diversity
Adaptive immunity
T cell receptor
TR repertoire analysis
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-015-0613-1