{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T11:46:28Z","timestamp":1784029588611,"version":"3.55.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2020,7,2]],"date-time":"2020-07-02T00:00:00Z","timestamp":1593648000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Austrian Science Fund","award":["T 974-B30"],"award-info":[{"award-number":["T 974-B30"]}]},{"name":"Austrian Science Fund","award":["I3978"],"award-info":[{"award-number":["I3978"]}]},{"name":"European Research Council","award":["786295"],"award-info":[{"award-number":["786295"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["TRR 241(INF)"],"award-info":[{"award-number":["TRR 241(INF)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Advances in single-cell technologies have enabled the investigation of T-cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T-cell receptors. Here, we propose single-cell immune repertoires in Python (Scirpy), a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Scirpy source code and documentation are available at https:\/\/github.com\/icbi-lab\/scirpy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa611","type":"journal-article","created":{"date-parts":[[2020,6,24]],"date-time":"2020-06-24T15:16:09Z","timestamp":1593011769000},"page":"4817-4818","source":"Crossref","is-referenced-by-count":181,"title":["Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data"],"prefix":"10.1093","volume":"36","author":[{"given":"Gregor","family":"Sturm","sequence":"first","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9745-6255","authenticated-orcid":false,"given":"Tamas","family":"Szabo","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"},{"name":"Biocenter, Institute of Developmental Immunology, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9659-4226","authenticated-orcid":false,"given":"Georgios","family":"Fotakis","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marlene","family":"Haider","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1754-690X","authenticated-orcid":false,"given":"Dietmar","family":"Rieder","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0636-7351","authenticated-orcid":false,"given":"Zlatko","family":"Trajanoski","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0712-4658","authenticated-orcid":false,"given":"Francesca","family":"Finotello","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,7,2]]},"reference":[{"key":"2023062213562989800_btaa611-B1","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"2023062213562989800_btaa611-B2","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2023062213562989800_btaa611-B3","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s12859-016-0930-z","article-title":"Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments","volume":"17","author":"Daily","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2023062213562989800_btaa611-B4","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nature22383","article-title":"Quantifiable predictive features define epitope-specific T cell receptor repertoires","volume":"547","author":"Dash","year":"2017","journal-title":"Nature"},{"key":"2023062213562989800_btaa611-B5","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1038\/s41576-019-0166-7","article-title":"Next-generation computational tools for interrogating cancer immunity","volume":"20","author":"Finotello","year":"2019","journal-title":"Nat. Rev. Genet"},{"key":"2023062213562989800_btaa611-B6","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nrg.2016.67","article-title":"Computational genomics tools for dissecting tumour\u2013immune cell interactions","volume":"17","author":"Hackl","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023062213562989800_btaa611-B7","doi-asserted-by":"crossref","DOI":"10.1002\/art.41252","article-title":"T-cell receptor immunosequencing reveals altered repertoire diversity and disease-associated clonal expansions in ankylosing spondylitis patients","author":"Hanson","year":"2020","journal-title":"Arthritis Rheumatol"},{"key":"2023062213562989800_btaa611-B8","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41590-020-0628-2","article-title":"Reverse TCR repertoire evolution toward dominant low-affinity clones during chronic cmv infection","volume":"21","author":"Schober","year":"2020","journal-title":"Nat. Immunol"},{"key":"2023062213562989800_btaa611-B9","doi-asserted-by":"crossref","first-page":"637","DOI":"10.4049\/jimmunol.1800904","article-title":"Dual TCR T cells: identity crisis or multitaskers?","volume":"202","author":"Schuldt","year":"2019","journal-title":"J. Immunol"},{"key":"2023062213562989800_btaa611-B10","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nmeth.3800","article-title":"T cell fate and clonality inference from single-cell transcriptomes","volume":"13","author":"Stubbington","year":"2016","journal-title":"Nat. Methods"},{"key":"2023062213562989800_btaa611-B11","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/s43018-019-0022-x","article-title":"Immune awakening revealed by peripheral T cell dynamics after one cycle of immunotherapy","volume":"1","author":"Valpione","year":"2020","journal-title":"Nat. Cancer"},{"key":"2023062213562989800_btaa611-B12","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.3389\/fimmu.2018.02206","article-title":"AIRR community standardized representations for annotated immune repertoires","volume":"9","author":"Vander Heiden","year":"2018","journal-title":"Front. Immunol"},{"key":"2023062213562989800_btaa611-B13","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"Scipy 1.0: fundamental algorithms for scientific computing in python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"2023062213562989800_btaa611-B14","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"Scanpy: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2023062213562989800_btaa611-B15","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1038\/s41586-020-2056-8","article-title":"Peripheral T cell expansion predicts tumour infiltration and clinical response","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa611\/33620207\/btaa611.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/18\/4817\/50677599\/btaa611.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/18\/4817\/50677599\/btaa611.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T15:09:19Z","timestamp":1687532959000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/18\/4817\/5866543"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,7,2]]},"references-count":15,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2020,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa611","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.04.10.035865","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,9,15]]},"published":{"date-parts":[[2020,7,2]]}}}