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PLoS Comput Biol. 2015 Nov 25;11(11):e1004503. doi: 10.1371/journal.pcbi.1004503. eCollection 2015 Nov.

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

Author information

1
Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia.
2
Pirogov Russian National Research Medical University, Moscow, Russia.
3
Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
4
National Research University Higher School of Economics, Moscow, Russia.
5
Russian Children's Hospital, Moscow, Russia.

Abstract

Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

PMID:
26606115
PMCID:
PMC4659587
DOI:
10.1371/journal.pcbi.1004503
[Indexed for MEDLINE]
Free PMC Article

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