EGSEA
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see EGSEA.
Ensemble of Gene Set Enrichment Analyses
Bioconductor version: 3.13
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 "4.1") 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 | 1.20.0 |
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_1.20.0.tar.gz |
Windows Binary | EGSEA_1.20.0.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | EGSEA_1.20.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/EGSEA |
Source Repository (Developer Access) | git clone git@git.bioconductor.org: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 3.13 | Source Archive |