UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C
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- dc.contributor.author Ramos-Rodríguez, Mireia
- dc.contributor.author Subirana-Granés, Marc
- dc.contributor.author Pasquali, Lorenzo
- dc.date.accessioned 2022-02-10T06:49:12Z
- dc.date.available 2022-02-10T06:49:12Z
- dc.date.issued 2021
- dc.description.abstract Motivation: 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. Results: 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. Availability: 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). Supplementary information: Supplementary data are available at Bioinformatics online.
- dc.description.sponsorship This work was supported by Spanish Ministry of Economy and Competiveness [SAF2017-86242-R], EFSD/JDRF/Lilly Programme on Type 1 Diabetes Research, ‘Unidad de Excelencia Maria de Maeztu’ [CEX2018-000792-M] and Premi Gonçal Lloveras i Vallès a l’Excelència en Investigació junior 2020.
- dc.format.mimetype application/pdf
- dc.identifier.citation Ramos-Rodríguez M, Subirana-Granés M, Pasquali L. UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C. Bioinformatics. 2021;37(22):4240-2. DOI: 10.1093/bioinformatics/btab392
- dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btab392
- dc.identifier.issn 1367-4803
- dc.identifier.uri http://hdl.handle.net/10230/52453
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Bioinformatics. 2021;37(22):4240-2
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/SAF2017-86242-R
- dc.rights © The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri https://creativecommons.org/licenses/by-nc/4.0/
- dc.title UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion