diffUTR

diffUTR: Streamlining differential exon and 3' UTR usage

Bioconductor version: Release (3.19)

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>

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

Installation

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


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Software
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
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
System Requirements
URL
Bug Reports	https://github.com/ETHZ-INS/diffUTR

Suggests	BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	diffUTR_1.12.0.tar.gz
Windows Binary (x86_64)	diffUTR_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	diffUTR_1.12.0.tgz
macOS Binary (arm64)	diffUTR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffUTR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/diffUTR
Bioc Package Browser	https://code.bioconductor.org/browse/diffUTR/
Package Short Url	https://bioconductor.org/packages/diffUTR/
Package Downloads Report	Download Stats