{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:56Z","timestamp":1772138096331,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,7]],"date-time":"2019-06-07T00:00:00Z","timestamp":1559865600000},"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\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["648050"],"award-info":[{"award-number":["648050"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"THREEDCELLPHYSICS"},{"DOI":"10.13039\/501100000265","name":"UK Medical Research Council","doi-asserted-by":"crossref","award":["MR\/J00913X\/1"],"award-info":[{"award-number":["MR\/J00913X\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]}],"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-C is a member of the chromosome-conformation-capture family of experimental methods which probes the 3D organization of chromosomes within the cell nucleus. It provides high-resolution information on the genome-wide chromatin interactions from a set of \u2018target\u2019 genomic locations, and is growing in popularity as a tool for improving our understanding of cis-regulation and gene function. Yet, analysis of the data is complicated, and to date there has been no dedicated or easy-to-use software to automate the process. We present capC-MAP, a software package for the analysis of Capture-C data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Implemented with both ease of use and flexibility in mind, capC-MAP is a suit of programs written in C++ and Python, where each program can be run separately, or an entire analysis can be performed with a single command line. It is available under an open-source licence at https:\/\/github.com\/cbrackley\/capC-MAP, as well as via the conda package manager, and should run on any standard Unix-style system.<\/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\/btz480","type":"journal-article","created":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T07:40:34Z","timestamp":1559634034000},"page":"4773-4775","source":"Crossref","is-referenced-by-count":16,"title":["capC-MAP: software for analysis of Capture-C data"],"prefix":"10.1093","volume":"35","author":[{"given":"Adam","family":"Buckle","sequence":"first","affiliation":[{"name":"Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital , Edinburgh EH4 2XU, UK"}]},{"given":"Nick","family":"Gilbert","sequence":"additional","affiliation":[{"name":"Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital , Edinburgh EH4 2XU, UK"}]},{"given":"Davide","family":"Marenduzzo","sequence":"additional","affiliation":[{"name":"SUPA, School of Physics and Astronomy, University of Edinburgh , Edinburgh EH9 3FD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5973-8179","authenticated-orcid":false,"given":"Chris A","family":"Brackley","sequence":"additional","affiliation":[{"name":"SUPA, School of Physics and Astronomy, University of Edinburgh , Edinburgh EH9 3FD, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,6,7]]},"reference":[{"key":"2023013108342812100_btz480-B1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1101\/gr.213066.116","article-title":"Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding","volume":"27","author":"Andrey","year":"2017","journal-title":"Genome Res"},{"key":"2023013108342812100_btz480-B2","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1016\/j.molcel.2018.09.016","article-title":"Polymer simulations of heteromorphic chromatin predict the 3-D folding of complex genomic loci","volume":"72","author":"Buckle","year":"2018","journal-title":"Mol. 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