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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_1.21.0.tar.gz |
| Windows Binary (x86_64) | diffUTR_1.21.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | diffUTR_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | diffUTR_1.21.0.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 |