rnaseqDTU
RNA-seq workflow for differential transcript usage following Salmon quantification
Bioconductor version: 3.24 · Package version: 1.33.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rnaseqDTU")Details
| Maintainer | Michael Love <michaelisaiahlove@gmail.com> |
| Author | Michael Love [aut, cre], Charlotte Soneson [aut], Rob Patro [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/thelovelab/rnaseqDTU/ |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow |
| Package Short Url | https://bioconductor.org/packages/rnaseqDTU/ |
Citation
From within R, enter citation("rnaseqDTU"):
Michael Love, Charlotte Soneson, Rob Patro. rnaseqDTU: RNA-seq workflow for differential transcript usage following Salmon quantification. doi:10.18129/B9.bioc.rnaseqDTU, R package version 1.33.0, https://bioconductor.org/packages/rnaseqDTU.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | rnaseqDTU_1.33.0.tar.gz |