EGSEA
This is the development version of EGSEA; for the stable release version, see EGSEA.
Ensemble of Gene Set Enrichment Analyses
Bioconductor version: Development (3.21)
This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.
Author: Monther Alhamdoosh [aut, cre], Luyi Tian [aut], Milica Ng [aut], Matthew Ritchie [ctb]
Maintainer: Monther Alhamdoosh <m.hamdoosh at gmail.com>
citation("EGSEA")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.35.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0), 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), htmlwidgets, plotly, DT |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | EGSEA123 |
| Imports Me | |
| Suggests Me | tidybulk, EGSEAdata |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EGSEA_1.35.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |