rnaseqDTU

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see rnaseqDTU.

RNA-seq workflow for differential transcript usage following Salmon quantification

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow

Version 1.18.0

License Artistic-2.0

Depends R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools

Imports

System Requirements

URL https://github.com/mikelove/rnaseqDTU/

Suggests knitr, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me

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Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package rnaseqDTU_1.18.0.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/

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