{"id":"https://openalex.org/W4309247727","doi":"https://doi.org/10.1093/bioinformatics/btac747","title":"htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets","display_name":"htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets","publication_year":2022,"publication_date":"2022-11-17","ids":{"openalex":"https://openalex.org/W4309247727","doi":"https://doi.org/10.1093/bioinformatics/btac747","pmid":"https://pubmed.ncbi.nlm.nih.gov/36394253"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac747","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac747","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac747/48520733/btac747.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/39/1/btac747/48520733/btac747.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007206948","display_name":"Sudeep Sahadevan","orcid":"https://orcid.org/0000-0003-2480-0937"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sudeep Sahadevan","raw_affiliation_strings":["Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069778577","display_name":"Thileepan Sekaran","orcid":"https://orcid.org/0000-0001-8227-3691"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thileepan Sekaran","raw_affiliation_strings":["Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022921072","display_name":"Nadia Ashaf","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nadia Ashaf","raw_affiliation_strings":["Directors' Research, Previously European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Directors' Research, Previously European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072320137","display_name":"Marko Fritz","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marko Fritz","raw_affiliation_strings":["Directors' Research, Previously European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Directors' Research, Previously European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000270755","display_name":"Matthias W. Hentze","orcid":"https://orcid.org/0000-0002-4023-7876"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias W Hentze","raw_affiliation_strings":["Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029601108","display_name":"Wolfgang Huber","orcid":"https://orcid.org/0000-0002-0474-2218"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wolfgang Huber","raw_affiliation_strings":["Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015392819","display_name":"Thomas Schwarzl","orcid":"https://orcid.org/0000-0001-7697-7000"},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Schwarzl","raw_affiliation_strings":["Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7697-7000","affiliations":[{"raw_affiliation_string":"Genome Biology / Directors' Research, European Molecular Biology Laboratory (EMBL) , Heidelberg 69117, Germany","institution_ids":["https://openalex.org/I4210138560"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007206948"],"corresponding_institution_ids":["https://openalex.org/I4210138560"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.0395,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.754407,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9157999753952026,"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/T10604","display_name":"RNA Research and Splicing","score":0.9157999753952026,"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/T12610","display_name":"RNA regulation and disease","score":0.019500000402331352,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.019099999219179153,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8859208822250366},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7464345693588257},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7440946698188782},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.7209077477455139},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6170014142990112},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5943711996078491},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4936703145503998},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.47550496459007263},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3602476716041565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35550040006637573},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3502516746520996},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3424023389816284},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13889247179031372}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8859208822250366},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7464345693588257},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7440946698188782},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.7209077477455139},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6170014142990112},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5943711996078491},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4936703145503998},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.47550496459007263},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3602476716041565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35550040006637573},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3502516746520996},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3424023389816284},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13889247179031372}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac747","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac747","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac747/48520733/btac747.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:36394253","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36394253","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:9825771","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825771","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/btac747","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac747","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac747/48520733/btac747.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":0.4300000071525574,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320338438","display_name":"HORIZON EUROPE Marie Sklodowska-Curie Actions","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309247727.pdf","grobid_xml":"https://content.openalex.org/works/W4309247727.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2010615446","https://openalex.org/W2102619694","https://openalex.org/W2107283247","https://openalex.org/W2134526812","https://openalex.org/W2138207763","https://openalex.org/W2171967549","https://openalex.org/W2179438025","https://openalex.org/W2307041907","https://openalex.org/W2342788749","https://openalex.org/W3106930452","https://openalex.org/W3133949585","https://openalex.org/W4221030787"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4386463918","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W3097598351","https://openalex.org/W2789551765","https://openalex.org/W3170192653","https://openalex.org/W4226320247"],"abstract_inverted_index":{"SUMMARY:":[0],"Transcriptome-wide":[1],"detection":[2],"of":[3,6,70],"binding":[4,72],"sites":[5],"RNA-binding":[7],"proteins":[8],"is":[9,81,102,108],"achieved":[10],"using":[11],"Individual-nucleotide":[12],"crosslinking":[13],"and":[14,17,36,63,89,106],"immunoprecipitation":[15],"(iCLIP)":[16],"its":[18],"derivative":[19],"enhanced":[20],"CLIP":[21],"(eCLIP)":[22],"sequencing":[23],"methods.":[24],"Here,":[25],"we":[26],"introduce":[27],"htseq-clip,":[28],"a":[29],"python":[30],"package":[31,46,79,86],"developed":[32],"for":[33,61],"preprocessing,":[34],"extracting":[35],"summarizing":[37],"crosslink":[38,48],"site":[39,49],"counts":[40],"from":[41],"i/eCLIP":[42],"experimental":[43],"data.":[44],"The":[45,77,100],"delivers":[47],"count":[50],"matrices":[51],"along":[52],"with":[53],"other":[54],"metrics,":[55],"which":[56],"can":[57],"be":[58],"directly":[59],"used":[60],"filtering":[62],"downstream":[64],"analyses":[65],"such":[66],"as":[67],"the":[68,90,95],"identification":[69],"differential":[71],"sites.":[73],"AVAILABILITY":[74],"AND":[75],"IMPLEMENTATION:":[76],"Python":[78],"htseq-clip":[80],"available":[82,109],"via":[83],"pypi":[84],"(python":[85],"index),":[87],"bioconda":[88],"Galaxy":[91],"Tool":[92],"Shed":[93],"under":[94,110],"open":[96],"source":[97],"MIT":[98],"License.":[99],"code":[101],"hosted":[103],"at":[104],"https://github.com/EMBL-Hentze-group/htseq-clip":[105],"documentation":[107],"https://htseq-clip.readthedocs.io/en/latest.":[111]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}