rnaseqDTU
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see rnaseqDTU.
RNA-seq workflow for differential transcript usage following Salmon quantification
Bioconductor version: 3.11
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("rnaseqDTU")):
Installation
To install this package, start R (version "4.0") 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 | 1.8.0 |
| 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/ |
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_1.8.0.tar.gz |
| Windows Binary | |
| macOS 10.13 (High Sierra) | |
| 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 |