{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T10:29:00Z","timestamp":1785148140946,"version":"3.55.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T00:00:00Z","timestamp":1564704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","award":["230338"],"award-info":[{"award-number":["230338"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Stiftelsen K.G. Jebsen"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and manipulating genomic intervals and their associated data in Python. Run single threaded on binary set operations, PyRanges is in median 2.3\u20139.6 times faster than the popular R GenomicRanges library and is equally memory efficient; run multi-threaded on 8 cores, our library is up to 123 times faster. PyRanges is therefore ideally suited both for individual analyses and as a foundation for future genomic libraries in Python.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PyRanges is available as open source under the MIT license at https:\/\/github.com\/biocore-NTNU\/pyranges and the documentation exists at https:\/\/biocore-NTNU.github.io\/pyranges\/<\/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\/btz615","type":"journal-article","created":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T07:13:48Z","timestamp":1564643628000},"page":"918-919","source":"Crossref","is-referenced-by-count":107,"title":["PyRanges: efficient comparison of genomic intervals in Python"],"prefix":"10.1093","volume":"36","author":[{"given":"Endre Bakken","family":"Stovner","sequence":"first","affiliation":[{"name":"Department of Computer Science , Trondheim 7013, Norway"},{"name":"Department of Clinical and Molecular Medicine , Trondheim 7013, Norway"},{"name":"Bioinformatics Core Facility , Trondheim 7013, Norway"},{"name":"Department of Public Health and Nursing , K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim 7013, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P\u00e5l","family":"S\u00e6trom","sequence":"additional","affiliation":[{"name":"Department of Computer Science , Trondheim 7013, Norway"},{"name":"Department of Clinical and Molecular Medicine , Trondheim 7013, Norway"},{"name":"Bioinformatics Core Facility , Trondheim 7013, Norway"},{"name":"Department of Public Health and Nursing , K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim 7013, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"key":"2023013110092497700_btz615-B1","doi-asserted-by":"crossref","first-page":"3423","DOI":"10.1093\/bioinformatics\/btr539","article-title":"Pybedtools: a flexible Python library for manipulating genomic datasets and annotations","volume":"27","author":"Dale","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013110092497700_btz615-B2","doi-asserted-by":"crossref","first-page":"R80.","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"2023013110092497700_btz615-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLoS Comput. 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