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.
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]
, Rafael Henkin [ctb, ths]
, Alfredo Iacoangeli [ctb, ths]
, Fabrizio Smeraldi [ctb, ths]
, Michael Barnes [ctb, ths]
Maintainer: Guy Hunt <guy.hunt at kcl.ac.uk>
citation("GEOexplorer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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
| Reference Manual |
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 |
See More
| Suggests | rmarkdown, usethis, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |