UMI4Cats

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see UMI4Cats.

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

Bioconductor version: 3.14

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 "4.1") 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 1.4.0

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, 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

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Package Archives

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

Source Package UMI4Cats_1.4.0.tar.gz

Windows Binary UMI4Cats_1.4.0.zip

macOS 10.13 (High Sierra) UMI4Cats_1.4.0.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/

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Old Source Packages for BioC 3.14 Source Archive