diffUTR
This is thereleased version of diffUTR; for the devel version, seediffUTR.
diffUTR: Streamlining differential exon and 3' UTR usage
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: 0000-0003-3418-4218, Stefan Gerber [aut]
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("diffUTR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("diffUTR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.18.0 |
| 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | diffUTR_1.18.0.tar.gz |
| Windows Binary (x86_64) | diffUTR_1.18.0.zip (64-bit only) |
| 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/ |
| Package Downloads Report | Download Stats |