Ramos-Rodríguez, MireiaSubirana-Granés, MarcPasquali, Lorenzo2022-02-102022-02-102021Ramos-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/btab3921367-4803http://hdl.handle.net/10230/52453Motivation: 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.application/pdfeng© 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.cominfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/bioinformatics/btab392info:eu-repo/semantics/openAccess