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categoryCompare

Meta-analysis of high-throughput experiments using feature annotations

Bioconductor version: 3.23 · Package version: 1.56.0

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

MaintainerRobert M. Flight <rflight79@gmail.com>
AuthorRobert M. Flight <rflight79@gmail.com>
LicenseGPL-2
URLhttps://github.com/rmflight/categoryCompare
Bug Reportshttps://github.com/rmflight/categoryCompare/issues
System RequirementsCytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested)
Downloads rank703
Source branchRELEASE_3_23
biocViewsAnnotation, GO, GeneExpression, MultipleComparison, Pathways, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagecategoryCompare_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