VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

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,...

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Bibliographic Details
Published in:PLoS computational biology Vol. 11; no. 11; p. e1004503
Main Authors: Shugay, Mikhail, Bagaev, Dmitriy V., Turchaninova, Maria A., Bolotin, Dmitriy A., Britanova, Olga V., Putintseva, Ekaterina V., Pogorelyy, Mikhail V., Nazarov, Vadim I., Zvyagin, Ivan V., Kirgizova, Vitalina I., Kirgizov, Kirill I., Skorobogatova, Elena V., Chudakov, Dmitriy M.
Format: Journal Article
Language:English
Published: United States Public Library of Science 01.11.2015
Public Library of Science (PLoS)
Subjects:
Adolescent
Adult
Aging
Analysis
Antigen receptors, T cell
Antigens
Child
Cluster Analysis
Computational Biology - methods
Genetic aspects
Genomics
Hematopoietic Stem Cell Transplantation
Humans
Lymphocytes
Multiple sclerosis
Multiple Sclerosis - genetics
Physiological aspects
Receptors
Receptors, Antigen, T-Cell - chemistry
Receptors, Antigen, T-Cell - genetics
Receptors, Antigen, T-Cell - metabolism
Sequence Analysis, DNA - methods
Similarity measures
Software
Software packages
Studies
T cell receptors
T cells
Twins - genetics
Young Adult
Russia
ISSN:1553-7358, 1553-734X, 1553-7358
Online Access:Get full text
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Description
Summary: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.
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Conceived and designed the experiments: MS DMC. Performed the experiments: MAT OVB EVP IVZ VIK KIK EVS. Analyzed the data: MS DVB DAB MVP VIN. Wrote the paper: MS DMC.
The authors have declared that no competing interests exist.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1004503