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GEOexplorer

This is the development version of GEOexplorer; for the stable release version, see GEOexplorer.

GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation

Bioconductor version: Development (3.18)

GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of gene expression analysis on microarray gene expression datasets held on the GEO database. The outputs are interactive graphs that enable users to explore the results of the 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] , Rafael Henkin [ctb, ths] , Fabrizio Smeraldi [ctb, ths] , Michael Barnes [ctb, ths]

Maintainer: Guy Hunt <guypwhunt1992 at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
my-vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, MicroRNAArray, Microarray, Software, mRNAMicroarray
Version 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License GPL-3
Depends shiny, limma, Biobase, plotly, shinyBS
Imports DT, htmltools, factoextra, heatmaply, maptools, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, utils
Linking To
Suggests rmarkdown, knitr, usethis, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/guypwhunt/GEOexplorer/
Bug Reports https://github.com/guypwhunt/GEOexplorer/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package GEOexplorer_1.7.0.tar.gz
Windows Binary GEOexplorer_1.7.0.zip
macOS Binary (x86_64) GEOexplorer_1.7.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/GEOexplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GEOexplorer
Bioc Package Browser https://code.bioconductor.org/browse/GEOexplorer/
Package Short Url https://bioconductor.org/packages/GEOexplorer/
Package Downloads Report Download Stats