VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

被引：436

作者：

Shugay, Mikhail ^{[1
,2
]}

Bagaev, Dmitriy V. ^{[1
]}

Turchaninova, Maria A. ^{[1
,2
]}

Bolotin, Dmitriy A. ^{[1
,2
]}

Britanova, Olga V. ^{[1
,2
,3
]}

Putintseva, Ekaterina V. ^{[1
,2
,3
]}

Pogorelyy, Mikhail V. ^{[1
]}

Nazarov, Vadim I. ^{[1
,4
]}

Zvyagin, Ivan V. ^{[1
,2
,3
]}

Kirgizova, Vitalina I. ^{[1
]}

Kirgizov, Kirill I. ^{[5
]}

Skorobogatova, Elena V. ^{[5
]}

Chudakov, Dmitriy M. ^{[1
,2
,3
]}

机构：

[1] RAS, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow 117901, Russia

[2] Pirogov Russian Natl Res Med Univ, Moscow, Russia

[3] Masaryk Univ, Cent European Inst Technol, Brno, Czech Republic

[4] Natl Res Univ, Higher Sch Econ, Moscow, Russia

[5] Russian Childrens Hosp, Moscow, Russia

来源：

PLOS COMPUTATIONAL BIOLOGY | 2015年 / 11卷 / 11期

基金：

俄罗斯科学基金会;

关键词：

RESIDUAL DISEASE DETECTION; MULTIPLE-SCLEROSIS; CLONAL EXPANSIONS; DEEP; DIVERSITY; GENERATION; SELECTION; SOFTWARE; OVERLAP; EPITOPE;

D O I：

10.1371/journal.pcbi.1004503

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：16

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