A B C E F G H K L M O P R S T misc
categoryCompare-package | Meta-analysis of high-throughput experiments using feature annotations |
allAnnotation | Class '"ccCompareResult"' |
allAnnotation-method | Class '"ccCompareResult"' |
annotation-method | Class '"ccSigList"' |
breakEdges | Break Cytoscape (or graphNEL) Network Edges |
breakEdges-method | Methods for Function 'breakEdges' in Package 'categoryCompare' |
breakEdges-methods | Methods for Function 'breakEdges' in Package 'categoryCompare' |
category-method | Class '"GENccEnrichResult"' |
category-method | Class '"ccSigList"' |
categoryCompare | Meta-analysis of high-throughput experiments using feature annotations |
ccCompare | Comparison of enriched annotations |
ccCompare-method | Comparison of enriched annotations |
ccCompare-methods | Comparison of enriched annotations |
ccCompareCollection | Class '"ccCompareCollection"' |
ccCompareCollection-class | Class '"ccCompareCollection"' |
ccCompareGeneric | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
ccCompareGeneric-method | Class '"GENccEnrichResult"' |
ccCompareGeneric-methods | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
ccCompareResult | Class '"ccCompareResult"' |
ccCompareResult-class | Class '"ccCompareResult"' |
ccData | Test data for 'categoryCompare' |
ccEnrich | Perform annotation enrichment for multiple gene lists |
ccEnrich-method | Perform annotation enrichment for multiple gene lists |
ccEnrichCollection | Class "ccEnrichCollection" |
ccEnrichCollection-class | Class "ccEnrichCollection" |
ccEnrichResult | Class "ccEnrichResult" |
ccEnrichResult-class | Class "ccEnrichResult" |
ccGeneList | Class "ccGeneList" |
ccGeneList-class | Class "ccGeneList" |
ccOptions | Class "ccOptions" |
ccOptions-class | Class "ccOptions" |
ccOptions-method | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
ccOpts | Test data for 'categoryCompare' |
ccOutCyt | Methods for Function 'ccOutCyt' in Package 'categoryCompare' |
ccOutCyt-method | Methods for Function 'ccOutCyt' in Package 'categoryCompare' |
ccOutCyt-methods | Methods for Function 'ccOutCyt' in Package 'categoryCompare' |
ccResults | Test data for 'categoryCompare' |
ccResultsBPHier | Test data for 'categoryCompare' |
ccSigList | Class '"ccSigList"' |
ccSigList-class | Class '"ccSigList"' |
ccType | Class "ccGeneList" |
ccType-method | Class "ccGeneList" |
ccType<- | Class "ccGeneList" |
ccType<--method | Class "ccGeneList" |
compareColors | Class "ccOptions" |
compareColors-method | Class "ccOptions" |
compareColors<- | Class "ccOptions" |
compareColors<--method | Class "ccOptions" |
compareIndx | Class "ccOptions" |
compareIndx-method | Class "ccOptions" |
compareNames | Class "ccOptions" |
compareNames-method | Class "ccOptions" |
compareNames<- | Class "ccOptions" |
compareNames<--method | Class "ccOptions" |
cssClass | Class "ccOptions" |
cssClass-method | Class "ccOptions" |
cwReload | Methods for Function 'cwReload' in Package 'categoryCompare' |
cwReload-method | Methods for Function 'cwReload' in Package 'categoryCompare' |
cwReload-methods | Methods for Function 'cwReload' in Package 'categoryCompare' |
cytOutData | Methods for Function 'cytOutData' |
cytOutData-method | Methods for Function 'cytOutData' |
cytOutData-methods | Methods for Function 'cytOutData' |
cytOutNodes | Methods for Function 'cytOutNodes' |
cytOutNodes-method | Methods for Function 'cytOutNodes' |
cytOutNodes-methods | Methods for Function 'cytOutNodes' |
enrichLists | Test data for 'categoryCompare' |
fdr | Number of FDR runs to perform |
fdr-method | Class "HyperGParamsCC" |
fdr-method | Class "HyperGResultCC" |
fdr-method | Class "ccEnrichResult" |
fdr-method | Class "ccGeneList" |
fdr<- | Number of FDR runs to perform |
fdr<--method | Class "HyperGParamsCC" |
fdr<--method | Class "ccGeneList" |
fdrvalues | Class "HyperGResultCC" |
fdrvalues-method | Class "HyperGResultCC" |
GENccEnrichResult | Class '"GENccEnrichResult"' |
GENccEnrichResult-class | Class '"GENccEnrichResult"' |
GENccEnrichResult-method | Methods for Function 'ccCompareGeneric' in Package 'categoryCompare' |
geneAnnMapping | Class '"GENccEnrichResult"' |
geneAnnMapping-method | Class '"GENccEnrichResult"' |
geneLists | Test data for 'categoryCompare' |
getAnnotation | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
getGeneName | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
getGeneSymbol | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
getGO2ALLEGS | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
getPATH2EG | Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion. |
GOccEnrichResult | Class "ccEnrichResult" |
GOccEnrichResult-class | Class "ccEnrichResult" |
GOHyperGParams | Class "HyperGParamsCC" |
GOHyperGParams-class | Class "HyperGParamsCC" |
GOHyperGParamsCC | Class "HyperGParamsCC" |
GOHyperGParamsCC-class | Class "HyperGParamsCC" |
GOHyperGResultCC | Class "HyperGResultCC" |
GOHyperGResultCC-class | Class "HyperGResultCC" |
graphType | graphType |
graphType-method | Class '"GENccEnrichResult"' |
graphType-method | Class "ccEnrichCollection" |
graphType-method | Class "ccEnrichResult" |
graphType-methods | graphType |
graphType<- | graphType |
graphType<--method | Class '"GENccEnrichResult"' |
graphType<--method | Class "ccEnrichCollection" |
graphType<--method | Class "ccEnrichResult" |
gseaRes | Test data for 'categoryCompare' |
gUniverse | Test data for 'categoryCompare' |
HyperGParamsCC | Class "HyperGParamsCC" |
HyperGParamsCC-class | Class "HyperGParamsCC" |
HyperGResultCC | Class "HyperGResultCC" |
HyperGResultCC-class | Class "HyperGResultCC" |
hyperGTestCC | Hypergeometric testing with false discovery rate |
hyperGTestCC,HyperGParamsCC | Hypergeometric testing with false discovery rate |
hyperGTestCC-method | Hypergeometric testing with false discovery rate |
KEGGccEnrichResult | Class "ccEnrichResult" |
KEGGccEnrichResult-class | Class "ccEnrichResult" |
KEGGHyperGParams | Class "HyperGParamsCC" |
KEGGHyperGParams-class | Class "HyperGParamsCC" |
KEGGHyperGParamsCC | Class "HyperGParamsCC" |
KEGGHyperGParamsCC-class | Class "HyperGParamsCC" |
KEGGHyperGResultCC | Class "HyperGResultCC" |
KEGGHyperGResultCC-class | Class "HyperGResultCC" |
listNames | listNames |
listNames-method | Class "ccGeneList" |
listNames-method | Class "ccOptions" |
listNames<--method | Class "ccOptions" |
mainGraph | Class '"ccCompareResult"' |
mainGraph-method | Class '"ccCompareResult"' |
mainTable | Class '"ccCompareResult"' |
mainTable-method | Class '"ccCompareResult"' |
mergedData-class | Class '"mergedData"' |
mergeLists | Function 'mergeLists' in Package 'categoryCompare' |
mergeLists-method | Function 'mergeLists' in Package 'categoryCompare' |
mergeLists-methods | Function 'mergeLists' in Package 'categoryCompare' |
minCount | minCount |
minCount-method | Class "HyperGResultCC" |
minCount-method | Class "ccEnrichResult" |
minCount<- | minCount |
minCount<--method | Class "HyperGResultCC" |
minCount<--method | Class "ccEnrichCollection" |
minCount<--method | Class "ccEnrichResult" |
minNodes | Delete nodes with less than a certain number of genes annotated |
minNodes-method | Delete nodes with less than a certain number of genes annotated |
ontology-method | Class '"GENccEnrichResult"' |
ontology-method | Class '"ccSigList"' |
organism-method | Class "HyperGParamsCC" |
outType | Class "ccOptions" |
outType-method | Class "ccOptions" |
outType<- | Class "ccOptions" |
outType<--method | Class "ccOptions" |
pCC-method | Class "HyperGResultCC" |
pvalueCutoff-method | Class "ccEnrichResult" |
pvalueCutoff-method | Class "ccGeneList" |
pvalueCutoff<--method | Class "HyperGResultCC" |
pvalueCutoff<--method | Class "ccEnrichCollection" |
pvalueCutoff<--method | Class "ccEnrichResult" |
pvalueCutoff<--method | Class "ccGeneList" |
pvalueType | Type of p-values to return from object |
pvalueType-method | Class "HyperGResultCC" |
pvalueType-method | Class "ccEnrichResult" |
pvalueType<- | Type of p-values to return from object |
pvalueType<--method | Class "HyperGResultCC" |
pvalueType<--method | Class "ccEnrichCollection" |
pvalueType<--method | Class "ccEnrichResult" |
resetColors | resetColors |
resetColors-method | resetColors |
resetColors-methods | resetColors |
show-method | Methods for Function show in Package 'categoryCompare' |
show-methods | Methods for Function show in Package 'categoryCompare' |
sigID | Class '"GENccEnrichResult"' |
sigID-method | Class '"ccSigList"' |
summary-method | Methods for Function show in Package 'categoryCompare' |
summary-methods | Methods for Function show in Package 'categoryCompare' |
table10 | Test data for 'categoryCompare' |
table48 | Test data for 'categoryCompare' |
testDirection-method | Class "ccGeneList" |
[-method | Class '"GENccEnrichResult"' |
[-method | Class "ccEnrichResult" |