UMI4Cats

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

Bioconductor version: Release (3.20)

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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("UMI4Cats")

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

Documentation

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

browseVignettes("UMI4Cats")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 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, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics
System Requirements
URL	https://github.com/Pasquali-lab/UMI4Cats
Bug Reports	https://github.com/Pasquali-lab/UMI4Cats/issues

Suggests	knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat
Linking To
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	UMI4Cats_1.16.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	UMI4Cats_1.16.0.tgz
macOS Binary (arm64)	UMI4Cats_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/UMI4Cats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/UMI4Cats
Bioc Package Browser	https://code.bioconductor.org/browse/UMI4Cats/
Package Short Url	https://bioconductor.org/packages/UMI4Cats/
Package Downloads Report	Download Stats