rnaseqDTU
RNA-seq workflow for differential transcript usage following Salmon quantification
Bioconductor version: Release (3.20)
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")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.25.0 |
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 | |
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Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | rnaseqDTU_1.25.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (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 |