augere.gsea
This is the development version of augere.gsea; to use it, please install the devel version of Bioconductor.
Automatic Generation of Gene Set Enrichment Analyses
Bioconductor version: Development (3.24)
Implements pipelines for generating gene set enrichment analysis reports in the augere framework. This includes various competitive and self-contained gene sets from a variety of Bioconductor packages. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce the gene set enrichment analysis.
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("augere.gsea")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("augere.gsea")
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("augere.gsea")| Gene set analyses | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneSetEnrichment, ReportWriting, Software, WorkflowManagement |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | stats, limma, S4Vectors, IRanges, augere.core, augere.de |
| System Requirements | |
| URL | https://github.com/augere-bioinfo/augere.gsea |
| Bug Reports | https://github.com/augere-bioinfo/augere.gsea/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, airway, goseq, fgsea, SummarizedExperiment, org.Hs.eg.db, GO.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | augere.gsea_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/augere.gsea |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/augere.gsea |
| Bioc Package Browser | https://code.bioconductor.org/browse/augere.gsea/ |
| Package Short Url | https://bioconductor.org/packages/augere.gsea/ |
| Package Downloads Report | Download Stats |