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categoryCompare (version 1.16.2)

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

1.16.2

License

GPL-2

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Maintainer

Robert M Flight

Last Published

February 15th, 2017

Functions in categoryCompare (1.16.2)

ccEnrichCollection-class

Class "ccEnrichCollection"
ccCompare-methods

Comparison of enriched annotations
ccOutCyt-methods

Methods for Function ccOutCyt in Package categoryCompare
ccCompareGeneric-methods

Methods for Function ccCompareGeneric in Package categoryCompare
hyperGTestCC

Hypergeometric testing with false discovery rate
ccCompareResult-class

Class "ccCompareResult"
cytOutNodes-methods

Methods for Function cytOutNodes
ccOptions-class

Class "ccOptions"
listNames

listNames
ccSigList-class

Class "ccSigList"
breakEdges

Break Cytoscape (or graphNEL) Network Edges
fdr

Number of FDR runs to perform
HyperGParamsCC-class

Class "HyperGParamsCC"
ccCompareCollection-class

Class "ccCompareCollection"
GENccEnrichResult-class

Class "GENccEnrichResult"
ccEnrich-method

Perform annotation enrichment for multiple gene lists
graphType-methods

graphType
ccGeneList-class

Class "ccGeneList"
minNodes

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

Methods for Function show in Package `categoryCompare'
getGeneSymbol

Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion.
categoryCompare-package

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

Methods for Function cytOutData
minCount

minCount
mergedData-class

Class "mergedData"
HyperGResultCC-class

Class "HyperGResultCC"
breakEdges-methods

Methods for Function breakEdges in Package categoryCompare
ccData

Test data for categoryCompare
ccEnrichResult-class

Class "ccEnrichResult"
mergeLists-methods

Function mergeLists in Package categoryCompare
pvalueType

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

Methods for Function cwReload in Package categoryCompare
resetColors-methods

resetColors