rnaseqDTU

RNA-seq workflow for differential transcript usage following Salmon quantification


Bioconductor version: Release (3.19)

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 (from within R, enter 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 1.24.0
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_1.24.0.tar.gz
Windows Binary
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