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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| Veröffentlicht in: | PLoS computational biology 2015-11, Vol.11 (11), p.e1004503-e1004503 |
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| container_issue | 11 |
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| creator | 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 |
| description | 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. |
| doi_str_mv | 10.1371/journal.pcbi.1004503 |
| format | Article |
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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. 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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, et al. (2015) VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. 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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.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Aging</subject><subject>Analysis</subject><subject>Antigen receptors, T cell</subject><subject>Antigens</subject><subject>Child</subject><subject>Cluster Analysis</subject><subject>Computational Biology - methods</subject><subject>Genetic aspects</subject><subject>Genomics</subject><subject>Hematopoietic Stem Cell Transplantation</subject><subject>Humans</subject><subject>Lymphocytes</subject><subject>Multiple sclerosis</subject><subject>Multiple Sclerosis - genetics</subject><subject>Physiological aspects</subject><subject>Receptors</subject><subject>Receptors, Antigen, T-Cell - chemistry</subject><subject>Receptors, Antigen, T-Cell - genetics</subject><subject>Receptors, Antigen, T-Cell - metabolism</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Similarity measures</subject><subject>Software</subject><subject>Software packages</subject><subject>Studies</subject><subject>T cell receptors</subject><subject>T cells</subject><subject>Twins - genetics</subject><subject>Young Adult</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>DOA</sourceid><recordid>eNqVUk2P0zAQjRCI_YB_gCBHOKTY8TeHRavyVbQCtBSu1sRxgqs0Dnayov8el2ZX2yP2waPxe29mnibLnmG0wETg1xs_hR66xWAqt8AIUYbIg-wUM0YKQZh8eC8-yc5i3CCUQsUfZycl54hjzE6ztz_ffR697-Kb_Efvmp3r2_ybj2MBSXsXXcx9k6_zpe26_NoaO4w-pGCwYfQu2Pgke9RAF-3T-T3P1h_er5efiquvH1fLy6vCMEbHAjdKCWGFVEiwEqhhDSgClbGVNFCrCowRhJOacSMJkgRTjmqFFS6xqIGcZy8OskPno55HjxoLqjhNRybE6oCoPWz0ENwWwk57cPpfwodWQxid6axOThlUcQS4Sq4ZXClTA0IWA2Uc4X21i7naVG1tbWw_BuiORI9_evdLt_5GU84UkyIJvJwFgv892TjqrYsmeQi99dO-byKpLEuJE3RxgLaQWnN945OiSbe2W2d8bxuX8peUCMRUiWgivDoiJMxo_4wtTDHq1ffr_8B-OcbSA9YEH2Owzd28GOn9xt3arvcbp-eNS7Tn9726I92uGPkL3CvRaQ</recordid><startdate>20151101</startdate><enddate>20151101</enddate><creator>Shugay, Mikhail</creator><creator>Bagaev, Dmitriy V</creator><creator>Turchaninova, Maria A</creator><creator>Bolotin, Dmitriy A</creator><creator>Britanova, Olga V</creator><creator>Putintseva, Ekaterina V</creator><creator>Pogorelyy, Mikhail V</creator><creator>Nazarov, Vadim I</creator><creator>Zvyagin, Ivan V</creator><creator>Kirgizova, Vitalina I</creator><creator>Kirgizov, Kirill I</creator><creator>Skorobogatova, Elena V</creator><creator>Chudakov, Dmitriy M</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISN</scope><scope>ISR</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20151101</creationdate><title>VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires</title><author>Shugay, Mikhail ; 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| 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 |
| title | VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires |
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