UMI4Cats

DOI: 10.18129/B9.bioc.UMI4Cats  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.8.1
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 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, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat
SystemRequirements
Enhances
URL	https://github.com/Pasquali-lab/UMI4Cats
BugReports	https://github.com/Pasquali-lab/UMI4Cats/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	UMI4Cats_1.8.1.tar.gz
Windows Binary	UMI4Cats_1.8.1.zip
macOS Binary (x86_64)	UMI4Cats_1.8.1.tgz
macOS Binary (arm64)	UMI4Cats_1.8.1.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
Old Source Packages for BioC 3.16	Source Archive