This is the development version of UMI4Cats; for the stable release version, see UMI4Cats.
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact dataBioconductor version: Development (3.22)
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] ORCID: 0000-0001-8083-2445 , Marc Subirana-Granes [aut], Lorenzo Pasquali [aut]
Maintainer: Mireia Ramos-Rodriguez <mireiarr9 at gmail.com>
Citation (from within R, entercitation("UMI4Cats")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("UMI4Cats")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("UMI4Cats")Follow Installation instructions to use this package in your R session.
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