categoryCompare: Meta-analysis of high-throughput experiments using feature annotations
Version 1.20.0

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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AuthorRobert M. Flight <rflight79@gmail.com>
Bioconductor views Annotation GO GeneExpression MultipleComparison Pathways
Date of publicationNone
MaintainerRobert M. Flight <rflight79@gmail.com>
LicenseGPL-2
Version1.20.0
URL https://github.com/rmflight/categoryCompare
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")

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'

Functions

GENccEnrichResult Man page
GENccEnrichResult,ccCompareGeneric-method Man page
GENccEnrichResult-class Man page
GOHyperGParams Man page
GOHyperGParams-class Man page
GOHyperGParamsCC Man page
GOHyperGParamsCC-class Man page
GOHyperGResultCC Man page
GOHyperGResultCC-class Man page
GOccEnrichResult Man page
GOccEnrichResult-class Man page
HyperGParamsCC Man page
HyperGParamsCC-class Man page
HyperGResultCC Man page
HyperGResultCC-class Man page
KEGGHyperGParams Man page
KEGGHyperGParams-class Man page
KEGGHyperGParamsCC Man page
KEGGHyperGParamsCC-class Man page
KEGGHyperGResultCC Man page
KEGGHyperGResultCC-class Man page
KEGGccEnrichResult Man page
KEGGccEnrichResult-class Man page
[,GENccEnrichResult,ANY,ANY,ANY-method Man page
[,GENccEnrichResult,ANY,ANY-method Man page
[,ccEnrichResult,ANY,ANY,ANY-method Man page
[,ccEnrichResult,ANY,ANY-method Man page
addListMembership Source code
allAnnotation Man page
allAnnotation,ccCompareResult-method Man page
annGenesComp Source code
annStatus Source code
annotateOutData Source code
annotation,ccSigList-method Man page
breakEdges Man page Source code
breakEdges,CytoscapeWindowClass,numeric-method Man page
breakEdges,ccCompareResult,numeric-method Man page
breakEdges-methods Man page
breakEdgesGraph Source code
category,GENccEnrichResult-method Man page
category,ccSigList-method Man page
categoryCompare Man page
categoryCompare-package Man page
ccCompare Man page Source code
ccCompare,GENccEnrichResult,ccOptions-method Man page
ccCompare,GOccEnrichResult,ccOptions-method Man page
ccCompare,KEGGccEnrichResult,ccOptions-method Man page
ccCompare,ccEnrichCollection,ccOptions-method Man page
ccCompare-methods Man page
ccCompareCollection Man page
ccCompareCollection-class Man page
ccCompareGO Source code
ccCompareGeneric Man page Source code
ccCompareGeneric,GENccEnrichResult,ccOptions-method Man page
ccCompareGeneric-methods Man page
ccCompareKEGG Source code
ccCompareResult Man page
ccCompareResult-class Man page
ccData Man page
ccEnrich Man page
ccEnrich,ccGeneList-method Man page
ccEnrich-method Man page
ccEnrichCollection Man page
ccEnrichCollection-class Man page
ccEnrichResult Man page
ccEnrichResult-class Man page
ccGeneList Man page
ccGeneList-class Man page
ccOptions Man page
ccOptions,ccCompareGeneric-method Man page
ccOptions-class Man page
ccOpts Man page
ccOutCyt Man page Source code
ccOutCyt,ccCompareResult,ccOptions-method Man page
ccOutCyt-methods Man page
ccResults Man page
ccResultsBPHier Man page
ccSigList Man page
ccSigList-class Man page
ccType Man page
ccType,ccGeneList-method Man page
ccType<- Man page
ccType<-,ccGeneList-method Man page
classGen Source code
colorData Source code
compData Source code
compMem Source code
compareColors Man page
compareColors,ccOptions-method Man page
compareColors<- Man page
compareColors<-,ccOptions-method Man page
compareIndx Man page
compareIndx,ccOptions-method Man page
compareNames Man page
compareNames,ccOptions-method Man page
compareNames<- Man page
compareNames<-,ccOptions-method Man page
createGraph Source code
createGraph2 Source code
cssClass Man page
cssClass,ccOptions-method Man page
cwReload Man page Source code
cwReload,CytoscapeWindowClass,character,ccOptions-method Man page
cwReload-methods Man page
cytOutData Man page Source code
cytOutData,list,ccCompareResult,mergedData-method Man page
cytOutData,list,ccCompareResult,missing-method Man page
cytOutData,list,missing,missing-method Man page
cytOutData-methods Man page
cytOutNodes Man page Source code
cytOutNodes,character,CytoscapeWindowClass,list-method Man page
cytOutNodes,character,CytoscapeWindowClass,missing-method Man page
cytOutNodes-methods Man page
enrichLists Man page
extractRes Source code
fdr Man page
fdr,HyperGParamsCC-method Man page
fdr,HyperGResultCC-method Man page
fdr,ccEnrichResult-method Man page
fdr,ccGeneList-method Man page
fdr<- Man page
fdr<-,HyperGParamsCC-method Man page
fdr<-,ccGeneList-method Man page
fdrvalues Man page
fdrvalues,HyperGResultCC-method Man page
fdrvalues-method Man page
gUniverse Man page
geneAnnMapping Man page
geneAnnMapping,GENccEnrichResult-method Man page
geneLists Man page
getAnnotation Man page Source code
getBar Source code
getDesc Source code
getEntrez Source code
getGO2ALLEGS Man page Source code
getGeneName Man page Source code
getGeneSymbol Man page Source code
getPATH2EG Man page Source code
goEnrich Source code
graphType Man page
graphType,GENccEnrichResult-method Man page
graphType,ccEnrichCollection-method Man page
graphType,ccEnrichResult-method Man page
graphType-methods Man page
graphType<- Man page
graphType<-,GENccEnrichResult-method Man page
graphType<-,ccEnrichCollection-method Man page
graphType<-,ccEnrichResult-method Man page
gseaRes Man page
headerOutData Source code
hyperGTestCC Man page
hyperGTestCC,HyperGParamsCC Man page
hyperGTestCC,HyperGParamsCC-method Man page
hyperGTestCat Source code
isPackageLoaded Source code
isResult Source code
keggEnrich Source code
listNames Man page
listNames,ccGeneList-method Man page
listNames,ccOptions-method Man page
listNames<-,ccOptions-method Man page
mainGraph Man page
mainGraph,ccCompareResult-method Man page
mainTable Man page
mainTable,ccCompareResult-method Man page
makeValidccLists Source code
makeValidccOptions Source code
mergeLists Man page Source code
mergeLists,ccGeneList,ccOptions-method Man page
mergeLists-methods Man page
mergedData-class Man page
minCount Man page
minCount,HyperGResultCC-method Man page
minCount,ccEnrichResult-method Man page
minCount<- Man page
minCount<-,HyperGResultCC-method Man page
minCount<-,ccEnrichCollection-method Man page
minCount<-,ccEnrichResult-method Man page
minNodes Man page Source code
minNodes,CytoscapeWindowClass,numeric-method Man page
moveTable Source code
nitGraphAtts Source code
nodeDat2Table Source code
ontology,GENccEnrichResult-method Man page
ontology,ccSigList-method Man page
outType Man page Source code
outType,ccOptions-method Man page
outType<- Man page
outType<-,ccOptions-method Man page
pCC,HyperGResultCC-method Man page
pvalueCutoff,ccEnrichResult-method Man page
pvalueCutoff,ccGeneList-method Man page
pvalueCutoff<-,HyperGResultCC-method Man page
pvalueCutoff<-,ccEnrichCollection-method Man page
pvalueCutoff<-,ccEnrichResult-method Man page
pvalueCutoff<-,ccGeneList-method Man page
pvalueType Man page
pvalueType,HyperGResultCC-method Man page
pvalueType,ccEnrichResult-method Man page
pvalueType<- Man page
pvalueType<-,HyperGResultCC-method Man page
pvalueType<-,ccEnrichCollection-method Man page
pvalueType<-,ccEnrichResult-method Man page
replaceCompareNames Source code
resetColors Man page Source code
resetColors,CytoscapeWindowClass,ccOptions-method Man page
resetColors-methods Man page
show,HyperGResultCC-method Man page
show-methods Man page
sigID Man page
sigID,ccSigList-method Man page
summary,HyperGResultCC-method Man page
summary-methods Man page
table10 Man page
table48 Man page
testDirection,ccGeneList-method Man page
visStatus Source code
whichCat Source code

Files

.BBSoptions
.Rinstignore
BUGS
DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.r
R/allGenerics.r
R/ccCompare.r
R/ccEnrichMethods.r
R/ccListsMethods.r
R/ccOptions.r
R/hyperGMethods.r
R/outCytoscape.r
R/showSummaryMethods.r
R/utils.r
R/variousAccessors.r
build
build/vignette.rds
data
data/ccData.RData
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/categoryCompare_vignette.R
inst/doc/categoryCompare_vignette.Rmd
inst/doc/categoryCompare_vignette.html
man
man/GENccEnrichResult-class.Rd
man/HyperGParamsCC-class.Rd
man/HyperGResultCC-class.Rd
man/breakEdges-methods.Rd
man/breakEdges.Rd
man/categoryCompare-package.Rd
man/ccCompare.Rd
man/ccCompareCollection-class.Rd
man/ccCompareGeneric-methods.Rd
man/ccCompareResult-class.Rd
man/ccData.Rd
man/ccEnrich.Rd
man/ccEnrichCollection-class.Rd
man/ccEnrichResult-class.Rd
man/ccGeneList-class.Rd
man/ccOptions-class.Rd
man/ccOutCyt-methods.Rd
man/ccSigList-class.Rd
man/cwReload-methods.Rd
man/cytOutData-methods.Rd
man/cytOutNodes-methods.Rd
man/fdr.Rd
man/getGeneSymbol.Rd
man/graphType-methods.Rd
man/hyperGTestCC.Rd
man/listNames.Rd
man/mergeLists-methods.Rd
man/mergedData-class.Rd
man/minCount.Rd
man/minNodes.Rd
man/pvalueType.Rd
man/resetColors-methods.Rd
man/show-methods.Rd
readme.md
vignettes
vignettes/BP2.png
vignettes/BP_8.png
vignettes/KEGG.png
vignettes/allEdges.png
vignettes/categoryCompare_vignette.Rmd
categoryCompare documentation built on May 20, 2017, 10:34 p.m.