{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:50Z","timestamp":1740185150636,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,2,9]],"date-time":"2018-02-09T00:00:00Z","timestamp":1518134400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2016-04911"],"award-info":[{"award-number":["RGPIN-2016-04911"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fonds de Recherche du Qu\u00e9bec-Sant\u00e9"},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Calcul Quebec and Compute Canada"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Chromatin state plays a major role in controlling gene expression, and comparative analysis of ChIP-seq data is key to understanding epigenetic regulation. We present chromswitch, an R\/Bioconductor package to integrate epigenomic data in a defined window of interest to detect an overall switch in chromatin state. Chromswitch accurately classifies a benchmarking dataset, and when applied genome-wide, the tool successfully detects chromatin changes that result in brain-specific expression.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Chromswitch is implemented as an R package available from Bioconductor at https:\/\/bioconductor.org\/packages\/chromswitch. All data and code for reproducing the analysis presented in this paper are available at https:\/\/doi.org\/10.5281\/zenodo.1101260.<\/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\/bty075","type":"journal-article","created":{"date-parts":[[2018,2,9]],"date-time":"2018-02-09T04:11:02Z","timestamp":1518149462000},"page":"2286-2288","source":"Crossref","is-referenced-by-count":11,"title":["chromswitch: a flexible method to detect chromatin state switches"],"prefix":"10.1093","volume":"34","author":[{"given":"Selin","family":"Jessa","sequence":"first","affiliation":[{"name":"Department of Human Genetics, McGill University, Montreal, QC, Canada and Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada"}]},{"given":"Claudia L","family":"Kleinman","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, McGill University, Montreal, QC, Canada and Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada"}]}],"member":"286","published-online":{"date-parts":[[2018,2,9]]},"reference":[{"key":"2023051604102457400_bty075-B1","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1093\/bioinformatics\/btv094","article-title":"A novel statistical method for quantitative comparison of multiple ChIP-seq datasets","volume":"31","author":"Chen","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051604102457400_bty075-B2","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat. 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