Category
This is the development version of Category; for the stable release version, see Category.
Category Analysis
Bioconductor version: Development (3.24)
A collection of tools for performing category (gene set enrichment) analysis.
Author: Robert Gentleman [aut], Seth Falcon [ctb], Deepayan Sarkar [ctb], Robert Castelo [ctb], Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("Category")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Category")
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("Category")| Using Categories to Analyze Microarray Data | R Script | |
| Using Chromosome Bands as Categories | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, GO, GeneSetEnrichment, Pathways, Software |
| Version | 2.79.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | Artistic-2.0 |
| Depends | methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix |
| Imports | utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI |
| System Requirements | |
| URL |
See More
| Suggests | EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db |
| Linking To | |
| Enhances | |
| Depends On Me | GOstats |
| Imports Me | categoryCompare, GmicR, meshr, miRLAB, phenoTest, scTensor |
| Suggests Me | qpgraph, RnBeads, maGUI |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Category_2.79.0.tar.gz |
| Windows Binary (x86_64) | Category_2.79.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Category_2.79.0.tgz |
| macOS Binary (sonoma-arm64) | Category_2.79.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Category |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Category |
| Bioc Package Browser | https://code.bioconductor.org/browse/Category/ |
| Package Short Url | https://bioconductor.org/packages/Category/ |
| Package Downloads Report | Download Stats |