rnaseqDTU

RNA-seq workflow for differential transcript usage following Salmon quantification

Bioconductor version: Release (3.17)

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 "4.3") 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

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Details

biocViews	GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow
Version	1.20.0
License	Artistic-2.0
Depends	R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools
Imports
Linking To
Suggests	knitr, rmarkdown
System Requirements
Enhances
URL	https://github.com/mikelove/rnaseqDTU/

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Package Archives

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

Source Package	rnaseqDTU_1.20.0.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