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UMI4Cats

This is the development version of UMI4Cats; for the stable release version, see UMI4Cats.

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

Bioconductor version: Development (3.18)

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 "4.3") 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.

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

Details

biocViews Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To
Suggests knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat
System Requirements
Enhances
URL https://github.com/Pasquali-lab/UMI4Cats
Bug Reports https://github.com/Pasquali-lab/UMI4Cats/issues
See More
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_1.11.0.tar.gz
Windows Binary UMI4Cats_1.11.0.zip (64-bit only)
macOS Binary (x86_64) UMI4Cats_1.11.0.tgz
macOS Binary (arm64)
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