DOI: 10.18129/B9.bioc.rnaseqDTU
This package is for version 3.14 of Bioconductor;
for the stable, up-to-date release version, see
rnaseqDTU.
RNA-seq workflow for differential transcript usage following Salmon quantification
Bioconductor version: 3.14
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
“4.1”) 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 |
Details
biocViews | GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow |
Version | 1.14.0 |
License | Artistic-2.0 |
Depends | R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools |
Imports | |
LinkingTo | |
Suggests | knitr, rmarkdown |
SystemRequirements | |
Enhances | |
URL | github.com/mikelove/rnaseqDTU/ |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me |
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