RnaSeqGeneEdgeRQL
Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This workflow package provides, through its vignette, a complete case study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes publication quality plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RnaSeqGeneEdgeRQL")Details
| Maintainer | Yunshun Chen <yuchen@wehi.edu.au> |
| Author | Yunshun Chen, Aaron Lun, Gordon Smyth |
| License | Artistic-2.0 |
| URL | http://f1000research.com/articles/5-1438/v2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow |
| Package Short Url | https://bioconductor.org/packages/RnaSeqGeneEdgeRQL/ |
Citation
From within R, enter citation("RnaSeqGeneEdgeRQL"):
Yunshun Chen, Aaron Lun, Gordon Smyth. RnaSeqGeneEdgeRQL: Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline. doi:10.18129/B9.bioc.RnaSeqGeneEdgeRQL, R package version 1.36.0, https://bioconductor.org/packages/RnaSeqGeneEdgeRQL.
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 | RnaSeqGeneEdgeRQL_1.36.0.tar.gz |
Dependencies
Depends: R (>= 3.3.0), edgeR (>= 4.3.6), gplots, org.Mm.eg.db, GO.db, BiocStyle
Suggests: knitr, knitcitations, rmarkdown