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UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Bioconductor version: Release (3.19)

UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.

Author: Mireia Ramos-Rodriguez [aut, cre] , Marc Subirana-Granes [aut], Lorenzo Pasquali [aut]

Maintainer: Mireia Ramos-Rodriguez <mireiarr9 at>

Citation (from within R, enter citation("UMI4Cats")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analyzing UMI-4C data with UMI4Cats HTML R Script
Reference Manual PDF


biocViews Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), SummarizedExperiment
Imports magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats,, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics
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Suggests knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat
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Follow Installation instructions to use this package in your R session.

Source Package UMI4Cats_1.14.0.tar.gz
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macOS Binary (x86_64) UMI4Cats_1.14.0.tgz
macOS Binary (arm64) UMI4Cats_1.14.0.tgz
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