{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T06:23:53Z","timestamp":1786083833509,"version":"3.56.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,9]],"date-time":"2019-09-09T00:00:00Z","timestamp":1567987200000},"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\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The most recent version of the package is available at https:\/\/github.com\/montilab\/hypeR.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz700","type":"journal-article","created":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T07:45:49Z","timestamp":1567669549000},"page":"1307-1308","source":"Crossref","is-referenced-by-count":181,"title":["hypeR: an R package for geneset enrichment workflows"],"prefix":"10.1093","volume":"36","author":[{"given":"Anthony","family":"Federico","sequence":"first","affiliation":[{"name":"Bioinformatics Department, Boston University , Boston, MA 02118, USA"},{"name":"Section of Computational Biomedicine, Boston University School of Medicine , Boston, MA 02118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Monti","sequence":"additional","affiliation":[{"name":"Bioinformatics Department, Boston University , Boston, MA 02118, USA"},{"name":"Section of Computational Biomedicine, Boston University School of Medicine , Boston, MA 02118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,9]]},"reference":[{"key":"2023013110161322600_btz700-B1","doi-asserted-by":"crossref","first-page":"D649.","DOI":"10.1093\/nar\/gkx1132","article-title":"The Reactome Pathway Knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023013110161322600_btz700-B2","doi-asserted-by":"crossref","first-page":"W90.","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013110161322600_btz700-B3","doi-asserted-by":"crossref","first-page":"1739.","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013110161322600_btz700-B4","author":"Mailund","year":"2017"},{"key":"2023013110161322600_btz700-B5","author":"Sergushichev","year":"2016"},{"key":"2023013110161322600_btz700-B6","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz700\/30062695\/btz700.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1307\/48982319\/btz700.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/4\/1307\/48982319\/btz700.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T13:28:50Z","timestamp":1675171730000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/4\/1307\/5566242"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,9,9]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz700","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/656637","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":[[2020,2,15]]},"published":{"date-parts":[[2019,9,9]]}}}