rnaseqDTU
This is the development version of rnaseqDTU; for the stable release version, see rnaseqDTU.
RNA-seq workflow for differential transcript usage following Salmon quantification
Bioconductor version: Development (3.24)
RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and DEXSeq to perform a DTU analysis on simulated data. It also shows how to use stageR to perform two-stage testing of DTU, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU.
Author: Michael Love [aut, cre], Charlotte Soneson [aut], Rob Patro [aut]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("rnaseqDTU")):
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("rnaseqDTU")
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("rnaseqDTU")| RNA-seq workflow for differential transcript usage following Salmon quantification | HTML | R Script |
Details
| biocViews | GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.33.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools |
| Imports | |
| System Requirements | |
| URL | https://github.com/thelovelab/rnaseqDTU/ |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rnaseqDTU_1.33.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/rnaseqDTU |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rnaseqDTU |
| Package Short Url | https://bioconductor.org/packages/rnaseqDTU/ |
| Package Downloads Report | Download Stats |