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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 (3.18)

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")

# 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

Reference Manual PDF

Details

biocViews GeneExpression, Software
Version 1.9.0
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
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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
Windows Binary diffUTR_1.9.0.zip
macOS Binary (x86_64) diffUTR_1.9.0.tgz
macOS Binary (arm64)
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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