diffUTR

DOI: 10.18129/B9.bioc.diffUTR    

This is the development version of diffUTR; for the stable release version, see diffUTR.

diffUTR: Streamlining differential exon and 3' UTR usage

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) diffUTR_1.3.0.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

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