Related Experiment Video
Updated: Nov 5, 2025
Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture 4C
Published on: April 29, 2020
UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C
Mireia Ramos-Rodríguez1, Marc Subirana-Granés1, Lorenzo Pasquali1
1Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, Barcelona 08003, Spain.
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.
