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categoryCompare (version 1.14.0)

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).

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Version

Version

1.14.0

License

GPL-2

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Maintainer

Robert M Flight

Last Published

February 15th, 2017

Functions in categoryCompare (1.14.0)

categoryCompare-package

Meta-analysis of high-throughput experiments using feature annotations
ccSigList-class

Class "ccSigList"
cwReload-methods

Methods for Function cwReload in Package categoryCompare
hyperGTestCC

Hypergeometric testing with false discovery rate
listNames

listNames
ccCompare-methods

Comparison of enriched annotations
ccEnrich-method

Perform annotation enrichment for multiple gene lists
ccEnrichCollection-class

Class "ccEnrichCollection"
cytOutNodes-methods

Methods for Function cytOutNodes
cytOutData-methods

Methods for Function cytOutData
minCount

minCount
minNodes

Delete nodes with less than a certain number of genes annotated
show-methods

Methods for Function show in Package `categoryCompare'
fdr

Number of FDR runs to perform
GENccEnrichResult-class

Class "GENccEnrichResult"
mergedData-class

Class "mergedData"
mergeLists-methods

Function mergeLists in Package categoryCompare
breakEdges

Break Cytoscape (or graphNEL) Network Edges
breakEdges-methods

Methods for Function breakEdges in Package categoryCompare
ccData

Test data for categoryCompare
ccCompareResult-class

Class "ccCompareResult"
ccCompareCollection-class

Class "ccCompareCollection"
ccCompareGeneric-methods

Methods for Function ccCompareGeneric in Package categoryCompare
ccEnrichResult-class

Class "ccEnrichResult"
ccGeneList-class

Class "ccGeneList"
getGeneSymbol

Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion.
graphType-methods

graphType
ccOptions-class

Class "ccOptions"
ccOutCyt-methods

Methods for Function ccOutCyt in Package categoryCompare
HyperGResultCC-class

Class "HyperGResultCC"
HyperGParamsCC-class

Class "HyperGParamsCC"
pvalueType

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

resetColors