{"id":"https://openalex.org/W3040324319","doi":"https://doi.org/10.1093/bioinformatics/btaa611","title":"Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data","display_name":"Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data","publication_year":2020,"publication_date":"2020-06-24","ids":{"openalex":"https://openalex.org/W3040324319","doi":"https://doi.org/10.1093/bioinformatics/btaa611","mag":"3040324319","pmid":"https://pubmed.ncbi.nlm.nih.gov/32614448"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa611","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa611","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4817/34560298/btaa611.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4817/34560298/btaa611.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052262434","display_name":"Gregor Sturm","orcid":"https://orcid.org/0000-0001-9584-7842"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Gregor Sturm","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051626236","display_name":"Tam\u00e1s Szab\u00f3","orcid":"https://orcid.org/0000-0001-9745-6255"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Tamas Szabo","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","Biocenter, Institute of Developmental Immunology, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]},{"raw_affiliation_string":"Biocenter, Institute of Developmental Immunology, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066001126","display_name":"Georgios Fotakis","orcid":"https://orcid.org/0000-0001-9659-4226"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Georgios Fotakis","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036701926","display_name":"Marlene Haider","orcid":"https://orcid.org/0000-0001-8214-6860"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Marlene Haider","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066477976","display_name":"Dietmar Rieder","orcid":"https://orcid.org/0000-0003-1754-690X"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Dietmar Rieder","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084751312","display_name":"Zlatko Trajanoski","orcid":"https://orcid.org/0000-0002-0636-7351"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Zlatko Trajanoski","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033275131","display_name":"Francesca Finotello","orcid":null},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Francesca Finotello","raw_affiliation_strings":["Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"],"affiliations":[{"raw_affiliation_string":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5033275131"],"corresponding_institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.1751,"has_fulltext":false,"cited_by_count":215,"citation_normalized_percentile":{"value":0.98093815,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"36","issue":"18","first_page":"4817","last_page":"4818"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8268336057662964},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7228716015815735},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6195731163024902},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6017622351646423},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5806477069854736},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.556371808052063},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48222053050994873},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.41130828857421875},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.343237042427063},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.27061405777931213},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20506200194358826},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18427541851997375},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.15720507502555847}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8268336057662964},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7228716015815735},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6195731163024902},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6017622351646423},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5806477069854736},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.556371808052063},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48222053050994873},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.41130828857421875},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.343237042427063},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27061405777931213},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20506200194358826},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18427541851997375},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15720507502555847}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa611","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa611","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4817/34560298/btaa611.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32614448","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32614448","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7751015","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7751015","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa611","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa611","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4817/34560298/btaa611.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6499999761581421,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G5125497749","display_name":null,"funder_award_id":"TRR 241(INF)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3040324319.pdf","grobid_xml":"https://content.openalex.org/works/W3040324319.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2260037449","https://openalex.org/W2295703274","https://openalex.org/W2461410982","https://openalex.org/W2671261300","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2893410333","https://openalex.org/W2902652978","https://openalex.org/W2914858428","https://openalex.org/W2972438906","https://openalex.org/W3003257820","https://openalex.org/W3005411249","https://openalex.org/W3007632958","https://openalex.org/W3010735835","https://openalex.org/W3011708550","https://openalex.org/W3103145119"],"related_works":["https://openalex.org/W4401741136","https://openalex.org/W2557718140","https://openalex.org/W4386470600","https://openalex.org/W4399490472","https://openalex.org/W2789551765","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W2491403535","https://openalex.org/W2479811461","https://openalex.org/W2104915799"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":43},{"year":2024,"cited_by_count":80},{"year":2023,"cited_by_count":37},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":5}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
