diffUTR

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

diffUTR: Streamlining differential exon and 3' UTR usage

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DOI: 10.18129/B9.bioc.diffUTR

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 iD 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")

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 1.18.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

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Build Report Build Report

Package Archives

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

Source Package diffUTR_1.18.0.tar.gz

Windows Binary (x86_64) diffUTR_1.17.0.zip

macOS Binary (x86_64) diffUTR_1.18.0.tgz

macOS Binary (arm64) diffUTR_1.18.0.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/

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