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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("categoryCompare")
AuthorRobert M. Flight <rflight79@gmail.com>
Bioconductor views Annotation GO GeneExpression MultipleComparison Pathways
Date of publicationNone
MaintainerRobert M. Flight <rflight79@gmail.com>
LicenseGPL-2
Version1.18.0
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'

Functions

allAnnotation Man page
allAnnotation,ccCompareResult-method Man page
annotation,ccSigList-method Man page
breakEdges Man page
breakEdges,ccCompareResult,numeric-method Man page
breakEdges,CytoscapeWindowClass,numeric-method Man page
breakEdges-methods Man page
category,ccSigList-method Man page
categoryCompare Man page
categoryCompare-package Man page
category,GENccEnrichResult-method Man page
ccCompare Man page
ccCompare,ccEnrichCollection,ccOptions-method Man page
ccCompareCollection Man page
ccCompareCollection-class Man page
ccCompare,GENccEnrichResult,ccOptions-method Man page
ccCompareGeneric Man page
ccCompareGeneric,GENccEnrichResult,ccOptions-method Man page
ccCompareGeneric-methods Man page
ccCompare,GOccEnrichResult,ccOptions-method Man page
ccCompare,KEGGccEnrichResult,ccOptions-method Man page
ccCompare-methods Man page
ccCompareResult Man page
ccCompareResult-class Man page
ccData Man page
ccEnrich Man page
ccEnrich,ccGeneList-method Man page
ccEnrichCollection Man page
ccEnrichCollection-class Man page
ccEnrich-method Man page
ccEnrichResult Man page
[,ccEnrichResult,ANY,ANY,ANY-method Man page
[,ccEnrichResult,ANY,ANY-method 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
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<- Man page
ccType<-,ccGeneList-method Man page
ccType,ccGeneList-method Man page
compareColors Man page
compareColors<- Man page
compareColors<-,ccOptions-method Man page
compareColors,ccOptions-method Man page
compareIndx Man page
compareIndx,ccOptions-method Man page
compareNames Man page
compareNames<- Man page
compareNames<-,ccOptions-method Man page
compareNames,ccOptions-method Man page
cssClass Man page
cssClass,ccOptions-method Man page
cwReload Man page
cwReload,CytoscapeWindowClass,character,ccOptions-method Man page
cwReload-methods Man page
cytOutData Man page
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
cytOutNodes,character,CytoscapeWindowClass,list-method Man page
cytOutNodes,character,CytoscapeWindowClass,missing-method Man page
cytOutNodes-methods Man page
enrichLists Man page
fdr Man page
fdr<- Man page
fdr,ccEnrichResult-method Man page
fdr<-,ccGeneList-method Man page
fdr,ccGeneList-method Man page
fdr<-,HyperGParamsCC-method Man page
fdr,HyperGParamsCC-method Man page
fdr,HyperGResultCC-method Man page
fdrvalues Man page
fdrvalues,HyperGResultCC-method Man page
fdrvalues-method Man page
GENccEnrichResult Man page
[,GENccEnrichResult,ANY,ANY,ANY-method Man page
[,GENccEnrichResult,ANY,ANY-method Man page
GENccEnrichResult,ccCompareGeneric-method Man page
GENccEnrichResult-class Man page
geneAnnMapping Man page
geneAnnMapping,GENccEnrichResult-method Man page
geneLists Man page
getAnnotation Man page
getGeneName Man page
getGeneSymbol Man page
getGO2ALLEGS Man page
getPATH2EG Man page
GOccEnrichResult Man page
GOccEnrichResult-class Man page
GOHyperGParams Man page
GOHyperGParamsCC Man page
GOHyperGParamsCC-class Man page
GOHyperGParams-class Man page
GOHyperGResultCC Man page
GOHyperGResultCC-class Man page
graphType Man page
graphType<- Man page
graphType<-,ccEnrichCollection-method Man page
graphType,ccEnrichCollection-method Man page
graphType<-,ccEnrichResult-method Man page
graphType,ccEnrichResult-method Man page
graphType<-,GENccEnrichResult-method Man page
graphType,GENccEnrichResult-method Man page
graphType-methods Man page
gseaRes Man page
gUniverse Man page
HyperGParamsCC Man page
HyperGParamsCC-class Man page
HyperGResultCC Man page
HyperGResultCC-class Man page
hyperGTestCC Man page
hyperGTestCC,HyperGParamsCC Man page
hyperGTestCC,HyperGParamsCC-method Man page
KEGGccEnrichResult Man page
KEGGccEnrichResult-class Man page
KEGGHyperGParams Man page
KEGGHyperGParamsCC Man page
KEGGHyperGParamsCC-class Man page
KEGGHyperGParams-class Man page
KEGGHyperGResultCC Man page
KEGGHyperGResultCC-class Man page
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
mergedData-class Man page
mergeLists Man page
mergeLists,ccGeneList,ccOptions-method Man page
mergeLists-methods Man page
minCount Man page
minCount<- Man page
minCount<-,ccEnrichCollection-method Man page
minCount<-,ccEnrichResult-method Man page
minCount,ccEnrichResult-method Man page
minCount<-,HyperGResultCC-method Man page
minCount,HyperGResultCC-method Man page
minNodes Man page
minNodes,CytoscapeWindowClass,numeric-method Man page
ontology,ccSigList-method Man page
ontology,GENccEnrichResult-method Man page
outType Man page
outType<- Man page
outType<-,ccOptions-method Man page
outType,ccOptions-method Man page
pCC,HyperGResultCC-method Man page
pvalueCutoff<-,ccEnrichCollection-method Man page
pvalueCutoff<-,ccEnrichResult-method Man page
pvalueCutoff,ccEnrichResult-method Man page
pvalueCutoff<-,ccGeneList-method Man page
pvalueCutoff,ccGeneList-method Man page
pvalueCutoff<-,HyperGResultCC-method Man page
pvalueType Man page
pvalueType<- Man page
pvalueType<-,ccEnrichCollection-method Man page
pvalueType<-,ccEnrichResult-method Man page
pvalueType,ccEnrichResult-method Man page
pvalueType<-,HyperGResultCC-method Man page
pvalueType,HyperGResultCC-method Man page
resetColors Man page
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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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