{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:58Z","timestamp":1772138098218,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T00:00:00Z","timestamp":1560470400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Babraham Institute Translational Advisory Group Award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Capture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package for robust detection of differential interactions in Capture Hi-C data. Chicdiff enhances a state-of-the-art differential testing approach for count data with bespoke normalization and multiple testing procedures that account for specific statistical properties of Capture Hi-C. We validate Chicdiff on published Promoter Capture Hi-C data in human Monocytes and CD4+ T cells, identifying multitudes of cell type-specific interactions, and confirming the overall positive association between promoter interactions and gene expression.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Chicdiff is implemented as an R package that is publicly available at https:\/\/github.com\/RegulatoryGenomicsGroup\/chicdiff.<\/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\/btz450","type":"journal-article","created":{"date-parts":[[2019,6,5]],"date-time":"2019-06-05T23:19:10Z","timestamp":1559776750000},"page":"4764-4766","source":"Crossref","is-referenced-by-count":29,"title":["Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data"],"prefix":"10.1093","volume":"35","author":[{"given":"Jonathan","family":"Cairns","sequence":"first","affiliation":[{"name":"Regulatory Genomics Group, Nuclear Dynamics Programme, Babraham Institute , Cambridge CB22 3AT, UK"},{"name":"Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca , Cambridge CB4 0WG, UK"}]},{"given":"William R","family":"Orchard","sequence":"additional","affiliation":[{"name":"Regulatory Genomics Group, Nuclear Dynamics Programme, Babraham Institute , Cambridge CB22 3AT, UK"},{"name":"Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences , London W12 0NN, UK"},{"name":"Institute of Clinical Sciences, Faculty of Medicine, Imperial College , London W12 0NN, UK"},{"name":"Department of Biochemistry, University of Cambridge , Cambridge CB2 1QW, UK"}]},{"given":"Valeriya","family":"Malysheva","sequence":"additional","affiliation":[{"name":"Regulatory Genomics Group, Nuclear Dynamics Programme, Babraham Institute , Cambridge CB22 3AT, UK"},{"name":"Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences , London W12 0NN, UK"},{"name":"Institute of Clinical Sciences, Faculty of Medicine, Imperial College , London W12 0NN, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0383-3943","authenticated-orcid":false,"given":"Mikhail","family":"Spivakov","sequence":"additional","affiliation":[{"name":"Regulatory Genomics Group, Nuclear Dynamics Programme, Babraham Institute , Cambridge CB22 3AT, UK"},{"name":"Functional Gene Control Group, Epigenetics Section, MRC London Institute of Medical Sciences , London W12 0NN, UK"},{"name":"Institute of Clinical Sciences, Faculty of Medicine, Imperial College , London W12 0NN, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,6,14]]},"reference":[{"key":"2023013108361043600_btz450-B1","doi-asserted-by":"crossref","first-page":"R106.","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023013108361043600_btz450-B2","doi-asserted-by":"crossref","first-page":"127.","DOI":"10.1186\/s13059-016-0992-2","article-title":"CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data","volume":"17","author":"Cairns","year":"2016","journal-title":"Genome Biol"},{"key":"2023013108361043600_btz450-B3","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":"2023013108361043600_btz450-B4","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s12864-018-5314-5","article-title":"Fine mapping chromatin contacts in capture Hi-C data","volume":"20","author":"Eijsbouts","year":"2019","journal-title":"BMC Genomics"},{"key":"2023013108361043600_btz450-B5","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/nmeth.3885","article-title":"Data-driven hypothesis weighting increases detection power in genome-scale multiple testing","volume":"13","author":"Ignatiadis","year":"2016","journal-title":"Nat. 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