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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 (3.19)

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 "4.4") 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

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 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
See More
Suggests BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
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Links To Me
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Package Archives

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

Source Package diffUTR_1.11.0.tar.gz
Windows Binary diffUTR_1.11.0.zip (64-bit only)
macOS Binary (x86_64) diffUTR_1.11.0.tgz
macOS Binary (arm64) diffUTR_1.11.0.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