diffUTR

DOI: 10.18129/B9.bioc.diffUTR    

diffUTR: Streamlining differential exon and 3' UTR usage

Bioconductor version: Release (3.13)

The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.

Author: Pierre-Luc Germain [cre, aut] , Stefan Gerber [aut]

Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("diffUTR")

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("diffUTR")

 

HTML	R Script	1_diffUTR
HTML	R Script	diffUTR_diffSplice2
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Software
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	GPL-3
Depends	R (>= 4.0)
Imports	S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite
LinkingTo
Suggests	BiocStyle, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/ETHZ-INS/diffUTR
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	diffUTR_1.0.0.tar.gz
Windows Binary	diffUTR_1.0.0.zip
macOS 10.13 (High Sierra)	diffUTR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffUTR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/diffUTR
Package Short Url	https://bioconductor.org/packages/diffUTR/
Package Downloads Report	Download Stats