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

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).

AuthorRobert M. Flight <rflight79@gmail.com>
Date of publicationNone
MaintainerRobert M. Flight <rflight79@gmail.com>
LicenseGPL-2
Version1.18.0
https://github.com/rmflight/categoryCompare

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

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