Learn R Programming

⚠️There's a newer version (1.16.2) of this package.Take me there.

categoryCompare (version 1.12.0)

Meta-analysis of high-throughput experiments using feature annotations

Description

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).

Copy Link

Version

Version

1.12.0

License

GPL-2

Issues

Pull Requests

Stars

Forks

Maintainer

Robert M Flight

Last Published

February 15th, 2017

Functions in categoryCompare (1.12.0)

HyperGParamsCC-class

Class "HyperGParamsCC"
HyperGResultCC-class

Class "HyperGResultCC"
ccCompareResult-class

Class "ccCompareResult"
categoryCompare-package

Meta-analysis of high-throughput experiments using feature annotations
cytOutData-methods

Methods for Function cytOutData
cytOutNodes-methods

Methods for Function cytOutNodes
ccCompare-methods

Comparison of enriched annotations
breakEdges-methods

Methods for Function breakEdges in Package categoryCompare
breakEdges

Break Cytoscape (or graphNEL) Network Edges
ccGeneList-class

Class "ccGeneList"
ccEnrichResult-class

Class "ccEnrichResult"
getGeneSymbol

Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion.
ccData

Test data for categoryCompare
ccSigList-class

Class "ccSigList"
cwReload-methods

Methods for Function cwReload in Package categoryCompare
minNodes

Delete nodes with less than a certain number of genes annotated
minCount

minCount
graphType-methods

graphType
ccCompareCollection-class

Class "ccCompareCollection"
ccCompareGeneric-methods

Methods for Function ccCompareGeneric in Package categoryCompare
ccOutCyt-methods

Methods for Function ccOutCyt in Package categoryCompare
ccOptions-class

Class "ccOptions"
mergedData-class

Class "mergedData"
mergeLists-methods

Function mergeLists in Package categoryCompare
pvalueType

Type of p-values to return from object
resetColors-methods

resetColors
ccEnrich-method

Perform annotation enrichment for multiple gene lists
ccEnrichCollection-class

Class "ccEnrichCollection"
fdr

Number of FDR runs to perform
GENccEnrichResult-class

Class "GENccEnrichResult"
listNames

listNames
hyperGTestCC

Hypergeometric testing with false discovery rate
show-methods

Methods for Function show in Package `categoryCompare'