categoryCompare
Meta-analysis of high-throughput experiments using feature annotations
Bioconductor version: 3.23 · Package version: 1.56.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("categoryCompare")Details
| Maintainer | Robert M. Flight <rflight79@gmail.com> |
| Author | Robert M. Flight <rflight79@gmail.com> |
| License | GPL-2 |
| URL | https://github.com/rmflight/categoryCompare |
| Bug Reports | https://github.com/rmflight/categoryCompare/issues |
| System Requirements | Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software |
| Package Short Url | https://bioconductor.org/packages/categoryCompare/ |
Citation
From within R, enter citation("categoryCompare"):
Robert M. Flight. categoryCompare: Meta-analysis of high-throughput experiments using feature annotations. doi:10.18129/B9.bioc.categoryCompare, R package version 1.56.0, https://bioconductor.org/packages/categoryCompare.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | categoryCompare_1.56.0.tar.gz |
| Windows binary (x86_64) | categoryCompare_1.56.0.zip |
| macOS binary (arm64) | categoryCompare_1.56.0.tgz |
| macOS binary (x86_64) | categoryCompare_1.56.0.tgz |
Dependencies
Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8)
Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils
Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown