{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T08:30:14Z","timestamp":1774773014981,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T00:00:00Z","timestamp":1668643200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EMBL Interdisciplinary Postdoc (EIPOD) programme under Marie Sklodowska-Curie Actions COFUND programme","award":["291772"],"award-info":[{"award-number":["291772"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Transcriptome-wide detection of binding sites of RNA-binding proteins is achieved using Individual-nucleotide crosslinking and immunoprecipitation (iCLIP) and its derivative enhanced CLIP (eCLIP) sequencing methods. Here, we introduce htseq-clip, a python package developed for preprocessing, extracting and summarizing crosslink site counts from i\/eCLIP experimental data. The package delivers crosslink site count matrices along with other metrics, which can be directly used for filtering and downstream analyses such as the identification of differential binding sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Python package htseq-clip is available via pypi (python package index), bioconda and the Galaxy Tool Shed under the open source MIT License. The code is hosted at https:\/\/github.com\/EMBL-Hentze-group\/htseq-clip and documentation is available under https:\/\/htseq-clip.readthedocs.io\/en\/latest.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac747","type":"journal-article","created":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T12:45:12Z","timestamp":1668689112000},"source":"Crossref","is-referenced-by-count":14,"title":["htseq-clip: a toolset for the preprocessing of eCLIP\/iCLIP datasets"],"prefix":"10.1093","volume":"39","author":[{"given":"Sudeep","family":"Sahadevan","sequence":"first","affiliation":[{"name":"Genome Biology \/ Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thileepan","family":"Sekaran","sequence":"additional","affiliation":[{"name":"Genome Biology \/ Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadia","family":"Ashaf","sequence":"additional","affiliation":[{"name":"Directors' Research, Previously European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marko","family":"Fritz","sequence":"additional","affiliation":[{"name":"Directors' Research, Previously European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias W","family":"Hentze","sequence":"additional","affiliation":[{"name":"Genome Biology \/ Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfgang","family":"Huber","sequence":"additional","affiliation":[{"name":"Genome Biology \/ Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7697-7000","authenticated-orcid":false,"given":"Thomas","family":"Schwarzl","sequence":"additional","affiliation":[{"name":"Genome Biology \/ Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,11,17]]},"reference":[{"key":"2023010805361729900_btac747-B1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2023010805361729900_btac747-B2","doi-asserted-by":"crossref","first-page":"R18","DOI":"10.1186\/gb-2014-15-1-r18","article-title":"PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis","volume":"15","author":"Chen","year":"2014","journal-title":"Genome Biol"},{"key":"2023010805361729900_btac747-B3","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/s41576-020-00302-y","article-title":"RNA-binding proteins in human genetic disease","volume":"22","author":"Gebauer","year":"2021","journal-title":"Nat. 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Methods"},{"key":"2023010805361729900_btac747-B11","doi-asserted-by":"crossref","first-page":"R8","DOI":"10.1186\/gb-2014-15-1-r8","article-title":"PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast","volume":"15","author":"Webb","year":"2014","journal-title":"Genome Biol"},{"key":"2023010805361729900_btac747-B12","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nmeth.3840","article-title":"irCLIP platform for efficient characterization of protein-RNA interactions","volume":"13","author":"Zarnegar","year":"2016","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac747\/48361906\/btac747.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac747\/48520733\/btac747.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac747\/48520733\/btac747.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T05:36:32Z","timestamp":1673156192000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac747\/6832040"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,11,17]]},"references-count":12,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac747","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,11,17]]},"article-number":"btac747"}}