diffUTR

DOI: 10.18129/B9.bioc.diffUTR    

diffUTR: Streamlining differential exon and 3' UTR usage

Bioconductor version: Release (3.15)

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 "4.2") 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")

 

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

Details

biocViews	GeneExpression, Software
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
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_1.4.0.tar.gz
Windows Binary	diffUTR_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	diffUTR_1.4.0.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