Bioconductor - diffUTR

This is the released version of diffUTR; for the devel version, see diffUTR.

diffUTR: Streamlining differential exon and 3' UTR usage

Bioconductor version: Release (3.22)

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] ORCID: 0000-0003-3418-4218 , 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 "4.5") 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")

Details

biocViews	GeneExpression, Software
Version	1.18.0
In Bioconductor since	BioC 3.13 (R-4.1) (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
System Requirements
URL
Bug Reports	https://github.com/ETHZ-INS/diffUTR

Package Archives

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