{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T08:23:16Z","timestamp":1774686196147,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,19]],"date-time":"2021-05-19T00:00:00Z","timestamp":1621382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Spanish Ministry of Economy and Competiveness","award":["SAF2017-86242-R"],"award-info":[{"award-number":["SAF2017-86242-R"]}]},{"name":"EFSD\/JDRF\/Lilly Programme on Type 1 Diabetes Research","award":["CEX2018-000792-M"],"award-info":[{"award-number":["CEX2018-000792-M"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>UMI-4C, a technique that combines chromosome conformation capture (4C) and unique molecular identifiers (UMI), is widely used to profile and quantitatively compare targeted chromosomal contact profiles. The analysis of UMI-4C experiments presents several computational challenges, including the removal of the PCR duplication bias and the identification of differential chromatin contacts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed UMI4Cats (UMI-4C Analysis Turned Simple), an R package that facilitates processing, analyzing and visualizing of data obtained by UMI-4C experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>UMI4Cats is implemented as an R package supported on Linux, MacOS and MS Windows. UMI4Cats is available from Bioconductor (https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/UMI4Cats.html) and GitHub (https:\/\/github.com\/Pasquali-lab\/UMI4Cats).<\/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\/btab392","type":"journal-article","created":{"date-parts":[[2021,5,18]],"date-time":"2021-05-18T19:12:03Z","timestamp":1621365123000},"page":"4240-4242","source":"Crossref","is-referenced-by-count":11,"title":["UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8083-2445","authenticated-orcid":false,"given":"Mireia","family":"Ramos-Rodr\u00edguez","sequence":"first","affiliation":[{"name":"Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra , Barcelona 08003, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3934-839X","authenticated-orcid":false,"given":"Marc","family":"Subirana-Gran\u00e9s","sequence":"additional","affiliation":[{"name":"Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra , Barcelona 08003, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2423-1826","authenticated-orcid":false,"given":"Lorenzo","family":"Pasquali","sequence":"additional","affiliation":[{"name":"Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra , Barcelona 08003, Spain"}]}],"member":"286","published-online":{"date-parts":[[2021,5,19]]},"reference":[{"key":"2023051607090006900_btab392-B1","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/nature23884","article-title":"The 4D nucleome project","volume":"549","author":"Dekker","year":"2017","journal-title":"Nature"},{"key":"2023051607090006900_btab392-B2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/s41576-019-0195-2","article-title":"Methods for mapping 3D chromosome architecture","volume":"21","author":"Kempfer","year":"2020","journal-title":"Nat. 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