Dataset Information
UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C.
Ontology highlight
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 and implementation
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.
SUBMITTER: Ramos-Rodriguez M
PROVIDER: S-EPMC9502148 | biostudies-literature | 2021 Nov
REPOSITORIES: biostudies-literature
Publications
UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C.
Bioinformatics (Oxford, England) 20211101 22
<h4>Motivation</h4>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.<h4>Results</h4>We have developed UMI4Cats (UMI-4C Analysis Turned Simple), an R package tha ...[more]
