UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C

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.