{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,30]],"date-time":"2024-04-30T00:34:45Z","timestamp":1714437285565},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,30]],"date-time":"2022-12-30T00:00:00Z","timestamp":1672358400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203151\/Z\/16\/Z","203151\/A\/16\/Z"],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UKRI Medical Research Council","award":["MC_PC_17230"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"Abstract<\/jats:title>\n Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.<\/jats:p>","DOI":"10.1093\/bib\/bbac591","type":"journal-article","created":{"date-parts":[[2022,12,30]],"date-time":"2022-12-30T12:32:05Z","timestamp":1672403525000},"source":"Crossref","is-referenced-by-count":4,"title":["bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data"],"prefix":"10.1093","volume":"24","author":[{"given":"Ilias","family":"Moutsopoulos","sequence":"first","affiliation":[{"name":"Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK"}]},{"given":"Eleanor C","family":"Williams","sequence":"additional","affiliation":[{"name":"Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-4863-761X","authenticated-orcid":false,"given":"Irina I","family":"Mohorianu","sequence":"additional","affiliation":[{"name":"Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK"}]}],"member":"286","published-online":{"date-parts":[[2022,12,30]]},"reference":[{"key":"2023011917115829600_ref1","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: the teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat Rev 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