GOstats
This is the released version of GOstats; for the devel version, see GOstats.
Tools for manipulating GO and microarrays
Bioconductor version: Release (3.23)
A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.
Author: Robert Gentleman [aut], Seth Falcon [ctb], Robert Castelo [ctb], Sonali Kumari [ctb] (Converted vignettes from Sweave to R Markdown / HTML.), Dennis Ndubi [ctb] (Converted GOstatsHyperG vignette from Sweave to R Markdown / HTML.), Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("GOstats")):
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("GOstats")
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("GOstats")| How To Use GOstats and Category to do Hypergeometric testing with unsupported model organisms | HTML | R Script |
| Hypergeometric Tests Using GOstats | HTML | R Script |
| Visualizing and Distances Using GO | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, MultipleComparison, Pathways, Software |
| Version | 2.78.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), Biobase(>= 1.15.29), Category(>= 2.43.2), graph |
| Imports | methods, stats, stats4, AnnotationDbi(>= 0.0.89), GO.db(>= 1.13.0), RBGL, annotate(>= 1.13.2), AnnotationForge, Rgraphviz |
| System Requirements | |
| URL |
See More
| Suggests | hgu95av2.db(>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | affycoretools, attract, categoryCompare, GmicR, ideal, miRLAB, pcaExplorer, scTensor |
| Suggests Me | a4, Category, fastLiquidAssociation, fgga, GSEAlm, MLP, qpgraph, RnBeads, safe, maGUI, sand |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GOstats_2.78.0.tar.gz |
| Windows Binary (x86_64) | GOstats_2.77.0.zip |
| macOS Binary (big-sur-x86_64) | GOstats_2.78.0.tgz |
| macOS Binary (sonoma-arm64) | GOstats_2.78.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GOstats |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GOstats |
| Bioc Package Browser | https://code.bioconductor.org/browse/GOstats/ |
| Package Short Url | https://bioconductor.org/packages/GOstats/ |
| Package Downloads Report | Download Stats |