GEOexplorer

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GEOexplorer.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

GEOexplorer: a webserver for gene expression analysis and visualisation

Bioconductor version: Release (3.23)

GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).

Author: Guy Hunt [aut, cre] ORCID: 0000-0002-5217-2678 , Rafael Henkin [ctb, ths] ORCID: 0000-0002-5511-5230 , Alfredo Iacoangeli [ctb, ths] ORCID: 0000-0002-5280-5017 , Fabrizio Smeraldi [ctb, ths] ORCID: 0000-0002-0057-8940 , Michael Barnes [ctb, ths] ORCID: 0000-0001-9097-7381

Maintainer: Guy Hunt <guy.hunt at kcl.ac.uk>

Citation (from within R, enter citation("GEOexplorer")):

Guy Hunt. GEOexplorer: GEOexplorer: a webserver for gene expression analysis and visualisation. doi:10.18129/B9.bioc.GEOexplorer, R package version 1.18.0, https://bioconductor.org/packages/GEOexplorer.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOexplorer")

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("GEOexplorer")

GEOexplorer	HTML
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, MicroRNAArray, Microarray, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (5 years)
License	GPL-3
Depends	shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0)
Imports	DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car
System Requirements
URL	https://github.com/guypwhunt/GEOexplorer/
Bug Reports	https://github.com/guypwhunt/GEOexplorer/issues

Suggests	rmarkdown, usethis, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/GEOexplorer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GEOexplorer
Package Short Url	https://bioconductor.org/packages/GEOexplorer/
Package Downloads Report	Download Stats