rnaseqDTU

 

RNA-seq workflow for differential transcript usage following Salmon quantification

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("rnaseqDTU", version = "3.8")

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")

 

HTML R Script RNA-seq workflow for differential transcript usage following Salmon quantification

Details

biocViews GeneExpressionWorkflow, Workflow
Version 1.0.0
License Artistic-2.0
Depends R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools
Imports
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/mikelove/rnaseqDTU/
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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/rnaseqDTU/
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