categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

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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).

Author
Robert M. Flight <rflight79@gmail.com>
Date of publication
None
Maintainer
Robert M. Flight <rflight79@gmail.com>
License
GPL-2
Version
1.18.0
URLs

View on Bioconductor

Man pages

breakEdges
Break Cytoscape (or graphNEL) Network Edges
breakEdges-methods
Methods for Function 'breakEdges' in Package...
categoryCompare-package
Meta-analysis of high-throughput experiments using feature...
ccCompare
Comparison of enriched annotations
ccCompareCollection-class
Class '"ccCompareCollection"'
ccCompareGeneric-methods
Methods for Function 'ccCompareGeneric' in Package...
ccCompareResult-class
Class '"ccCompareResult"'
ccData
Test data for 'categoryCompare'
ccEnrich
Perform annotation enrichment for multiple gene lists
ccEnrichCollection-class
Class "ccEnrichCollection"
ccEnrichResult-class
Class "ccEnrichResult"
ccGeneList-class
Class "ccGeneList"
ccOptions-class
Class "ccOptions"
ccOutCyt-methods
Methods for Function 'ccOutCyt' in Package 'categoryCompare'
ccSigList-class
Class '"ccSigList"'
cwReload-methods
Methods for Function 'cwReload' in Package 'categoryCompare'
cytOutData-methods
Methods for Function 'cytOutData'
cytOutNodes-methods
Methods for Function 'cytOutNodes'
fdr
Number of FDR runs to perform
GENccEnrichResult-class
Class '"GENccEnrichResult"'
getGeneSymbol
Entrez to name, symbol, GO and path conversion, as well as...
graphType-methods
graphType
HyperGParamsCC-class
Class "HyperGParamsCC"
HyperGResultCC-class
Class "HyperGResultCC"
hyperGTestCC
Hypergeometric testing with false discovery rate
listNames
listNames
mergedData-class
Class '"mergedData"'
mergeLists-methods
Function 'mergeLists' in Package 'categoryCompare'
minCount
minCount
minNodes
Delete nodes with less than a certain number of genes...
pvalueType
Type of p-values to return from object
resetColors-methods
resetColors
show-methods
Methods for Function show in Package 'categoryCompare'

Files in this package

categoryCompare/.BBSoptions
categoryCompare/.Rinstignore
categoryCompare/BUGS
categoryCompare/DESCRIPTION
categoryCompare/NAMESPACE
categoryCompare/NEWS
categoryCompare/R
categoryCompare/R/allClasses.r
categoryCompare/R/allGenerics.r
categoryCompare/R/ccCompare.r
categoryCompare/R/ccEnrichMethods.r
categoryCompare/R/ccListsMethods.r
categoryCompare/R/ccOptions.r
categoryCompare/R/hyperGMethods.r
categoryCompare/R/outCytoscape.r
categoryCompare/R/showSummaryMethods.r
categoryCompare/R/utils.r
categoryCompare/R/variousAccessors.r
categoryCompare/build
categoryCompare/build/vignette.rds
categoryCompare/data
categoryCompare/data/ccData.RData
categoryCompare/data/datalist
categoryCompare/inst
categoryCompare/inst/CITATION
categoryCompare/inst/doc
categoryCompare/inst/doc/categoryCompare_vignette.R
categoryCompare/inst/doc/categoryCompare_vignette.Rmd
categoryCompare/inst/doc/categoryCompare_vignette.html
categoryCompare/man
categoryCompare/man/GENccEnrichResult-class.Rd
categoryCompare/man/HyperGParamsCC-class.Rd
categoryCompare/man/HyperGResultCC-class.Rd
categoryCompare/man/breakEdges-methods.Rd
categoryCompare/man/breakEdges.Rd
categoryCompare/man/categoryCompare-package.Rd
categoryCompare/man/ccCompare.Rd
categoryCompare/man/ccCompareCollection-class.Rd
categoryCompare/man/ccCompareGeneric-methods.Rd
categoryCompare/man/ccCompareResult-class.Rd
categoryCompare/man/ccData.Rd
categoryCompare/man/ccEnrich.Rd
categoryCompare/man/ccEnrichCollection-class.Rd
categoryCompare/man/ccEnrichResult-class.Rd
categoryCompare/man/ccGeneList-class.Rd
categoryCompare/man/ccOptions-class.Rd
categoryCompare/man/ccOutCyt-methods.Rd
categoryCompare/man/ccSigList-class.Rd
categoryCompare/man/cwReload-methods.Rd
categoryCompare/man/cytOutData-methods.Rd
categoryCompare/man/cytOutNodes-methods.Rd
categoryCompare/man/fdr.Rd
categoryCompare/man/getGeneSymbol.Rd
categoryCompare/man/graphType-methods.Rd
categoryCompare/man/hyperGTestCC.Rd
categoryCompare/man/listNames.Rd
categoryCompare/man/mergeLists-methods.Rd
categoryCompare/man/mergedData-class.Rd
categoryCompare/man/minCount.Rd
categoryCompare/man/minNodes.Rd
categoryCompare/man/pvalueType.Rd
categoryCompare/man/resetColors-methods.Rd
categoryCompare/man/show-methods.Rd
categoryCompare/readme.md
categoryCompare/vignettes
categoryCompare/vignettes/BP2.png
categoryCompare/vignettes/BP_8.png
categoryCompare/vignettes/KEGG.png
categoryCompare/vignettes/allEdges.png
categoryCompare/vignettes/categoryCompare_vignette.Rmd