GEOexplorer

DOI: 10.18129/B9.bioc.GEOexplorer    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	my-vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, MicroRNAArray, Microarray, Software, mRNAMicroarray
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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
LinkingTo
Suggests	rmarkdown, knitr, usethis, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/guypwhunt/GEOexplorer/
BugReports	https://github.com/guypwhunt/GEOexplorer/issues
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_1.2.0.tar.gz
Windows Binary	GEOexplorer_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	GEOexplorer_1.2.0.tgz
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