EGSEA
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EGSEA.
Ensemble of Gene Set Enrichment Analyses
Bioconductor version: 3.9
This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.
Author: Monther Alhamdoosh, Luyi Tian, Milica Ng and Matthew Ritchie
Maintainer: Monther Alhamdoosh <m.hamdoosh at gmail.com>
Citation (from within R, enter
citation("EGSEA")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("EGSEA")
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("EGSEA")| EGSEA vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, GeneSignaling, GeneTarget, Genetics, GraphAndNetwork, ImmunoOncology, KEGG, Metabolomics, Microarray, MultipleComparison, Network, NetworkEnrichment, OneChannel, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, TwoChannel |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), Biobase, gage(>= 2.14.4), AnnotationDbi, topGO(>= 2.16.0), pathview(>= 1.4.2) |
| Imports | PADOG(>= 1.6.0), GSVA(>= 1.12.0), globaltest(>= 5.18.0), limma(>= 3.20.9), edgeR(>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe(>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata(>= 1.3.1), Glimma(>= 1.4.0), htmlwidgets, plotly, DT |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | EGSEA123 |
| Imports Me | |
| Suggests Me | EGSEAdata |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EGSEA_1.12.0.tar.gz |
| Windows Binary | EGSEA_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | EGSEA_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/EGSEA |
| Source Repository (Developer Access) | git clone [email protected]:packages/EGSEA |
| Bioc Package Browser | https://code.bioconductor.org/browse/EGSEA/ |
| Package Short Url | https://bioconductor.org/packages/EGSEA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |