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

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

Author information

1
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. vdm.nazarov@gmail.com.
2
National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia. vdm.nazarov@gmail.com.
3
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. m.pogorely@gmail.com.
4
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. ekomech@gmail.com.
5
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. izvyagin@gmail.com.
6
Central European Institute of Technology, Masaryk University, Brno, Czech Republic. izvyagin@gmail.com.
7
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. bolotin.dmitriy@gmail.com.
8
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. mikhail.shugay@gmail.com.
9
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. chudakovdm@mail.ru.
10
Central European Institute of Technology, Masaryk University, Brno, Czech Republic. chudakovdm@mail.ru.
11
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. lebedev_yb@ibch.ru.
12
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. imamedov78@gmail.com.

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 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.

PMID:
26017500
PMCID:
PMC4445501
DOI:
10.1186/s12859-015-0613-1
[Indexed for MEDLINE]
Free PMC Article

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