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 (3.20)
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("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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Software |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | diffUTR_1.13.0.tar.gz |
| Windows Binary (x86_64) | diffUTR_1.13.0.zip |
| macOS Binary (x86_64) | diffUTR_1.13.0.tgz |
| macOS Binary (arm64) | diffUTR_1.13.0.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 |