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diffUTR

diffUTR: Streamlining differential exon and 3' UTR usage

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews GeneExpression, Software
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
Linking To
Suggests BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports https://github.com/ETHZ-INS/diffUTR
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 diffUTR_1.8.0.tar.gz
Windows Binary diffUTR_1.8.0.zip (64-bit only)
macOS Binary (x86_64) diffUTR_1.8.0.tgz
macOS Binary (arm64) diffUTR_1.8.0.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