UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C.
basic_science · Level V
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- Record sourced from PubMed, PMID 34009302.
- Also identified by DOI 10.1093/bioinformatics/btab392 and PMC identifier 9502148.
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Abstract
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. 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. 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 data are available at Bioinformatics online.
Medical subject headings
- Chromatin
- Software