WGCNA
Weighted Correlation Network Analysis

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662
Source code
56
Man pages
233
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WGCNA: Weighted Correlation Network Analysis
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API

API for WGCNA
Weighted Correlation Network Analysis

Global functions
.Average Source code
.ClusterCoef.fun Source code
.MAR Source code
.MaxMean Source code
.MinMean Source code
.NPC.direct Source code
.NPC.iterate Source code
.absMaxMean Source code
.absMinMean Source code
.accuracyStatistics Source code
.alignedFirstPC Source code
.autoTicks Source code
.bicov Source code
.boxDimensionsForHeatmapWithLegend Source code
.branchCritFromStabilityLabels Source code
.calculateIndicator Source code
.causalChildren Source code
.checkAdj Source code
.checkAndDelete Source code
.checkAndScaleMultiWeights Source code
.checkAndScaleWeights Source code
.checkAvailableMemory Source code
.checkComponents Source code
.checkConsistencyOfGroupAndColID Source code
.checkExpr Source code
.checkListDimConsistencyAndGetDimnames Source code
.checkListNamesConsistency Source code
.checkLogicalConsistency Source code
.checkPower Source code
.choosenew Source code
.clustOrder Source code
.clusterCoeff Source code
.colWeightedMeans.x Source code
.colWeightedVars Source code
.collect_garbage Source code
.combineAdj Source code
.computeLinksInNeighbors Source code
.computeSqDiagSum Source code
.consensusCalculation.base Source code
.consensusCalculation.base.FromList Source code
.consensusMEDissimilarity Source code
.corCalculation Source code
.corWeighted Source code
.corWeighted.new Source code
.coreCalcForAdj Source code
.coreCalcForExpr Source code
.cr.MaxMean Source code
.cr.MinMean Source code
.cr.absMaxMean Source code
.cr.absMinMean Source code
.cr.maxVariance Source code
.cvPresent Source code
.devianceResidual Source code
.dimensions Source code
.dropThirdDim Source code
.effectiveNChar Source code
.emptyDist Source code
.equalizeQuantiles Source code
.err.bp Source code Source code
.euclideanDist.forNCP Source code
.extend Source code
.filterSimilarPS Source code
.getAttributesOrEmptyList Source code
.getBDorPlainData Source code
.getBranchMembers Source code
.getData Source code
.getElement Source code
.getSVDs Source code
.heatmapWithLegend Source code
.hierarchicalConsensusMEDissimilarity Source code
.histogramsWithCommonBreaks Source code
.initialFit.defaultOptions Source code
.initialFit.defaultWeightName Source code
.initialFit.requiresFormula Source code
.interleave Source code
.is.adjmat Source code
.isBinary Source code
.isNumericVector Source code
.kIM Source code
.linearModelCoefficients Source code
.listRep Source code
.loadAsList Source code
.loadObject Source code
.maxRowVariance Source code
.meanInRange Source code
.mergeConsensusTOMInformationLists Source code
.minTreeHeight Source code
.modulePreservationInternal Source code
.mtd.checkDimConsistencyAndGetDimnames Source code
.multiPlot Source code
.nNAColors Source code
.nProcessorsOnline Source code
.networkCalculation Source code
.offDiagonalMatrixSum Source code
.onAttach Source code
.orderLabelsBySize Source code
.pValueFromZ Source code
.panel.cor Source code
.panel.hist Source code
.permissiveDim Source code
.plotColorLegend Source code
.plotDendrogram Source code
.plotOrderedColorSubplot Source code
.plotStandaloneLegend Source code
.processFileName Source code
.qValueFromP Source code
.qorder Source code
.quickGeneVotingPredictor Source code
.quickGeneVotingPredictor.CV Source code
.restrictIndex Source code
.reverseRows Source code
.saveChunks Source code
.selectFewestMissing Source code
.setAttr Source code
.setAttrFromList Source code
.shiftList Source code
.sizeDependentQuantile Source code
.substituteTags Source code
.table2.allLevels Source code
.transformCoordinates Source code
.turnDistVectorIntoMatrix Source code
.turnVectorIntoDist Source code
.useDiskCache Source code
.useNThreads Source code
.vector2dist Source code
.weightedScale Source code
.weightedVar Source code
AFcorMI Man page Source code
BD.actualFileNames Man page Source code
BD.blockLengths Man page Source code
BD.checkAndDeleteFiles Man page Source code
BD.getData Man page Source code
BD.getMetaData Man page Source code
BD.nBlocks Man page Source code
BlockInformation Man page
BlockwiseData Man page
BloodLists Man page
BrainLists Man page
BrainRegionMarkers Man page
ConsensusOptions Man page
ConsensusTree Man page
CorrelationOptions Man page
GOenrichmentAnalysis Man page Source code
GTOMdist Man page Source code
ImmunePathwayLists Man page
NetworkOptions Man page
PWLists Man page
SCsLists Man page
TOMdist Man page Source code
TOMplot Man page Source code
TOMsimilarity Man page Source code
TOMsimilarityFromExpr Man page Source code
TrueTrait Man page Source code
WGCNAnThreads Man page Source code
accuracyMeasures Man page Source code
addBlockToBlockwiseData Man page Source code
addErrorBars Man page Source code
addGrid Man page Source code
addGuideLines Man page Source code
addTraitToMEs Man page Source code
adjacency Man page Source code
adjacency.fromSimilarity Man page Source code
adjacency.polyReg Man page Source code
adjacency.splineReg Man page Source code
alignExpr Man page Source code
allocateJobs Man page Source code
allowWGCNAThreads Man page Source code
automaticNetworkScreening Man page Source code
automaticNetworkScreeningGS Man page Source code
bicor Man page Source code
bicorAndPvalue Man page Source code
bicovWeightFactors Man page Source code
bicovWeights Man page Source code
bicovWeightsFromFactors Man page Source code
binarizeCategoricalColumns Man page Source code
binarizeCategoricalColumns.forPlots Man page Source code
binarizeCategoricalColumns.forRegression Man page Source code
binarizeCategoricalColumns.pairwise Man page Source code
binarizeCategoricalVariable Man page Source code
blockSize Man page Source code
blockwiseConsensusModules Man page Source code
blockwiseIndividualTOMs Man page Source code
blockwiseModules Man page Source code
blueWhiteRed Man page Source code
branchEigengeneDissim Man page Source code
branchEigengeneSimilarity Man page Source code
branchSplit Man page Source code
branchSplit.dissim Man page Source code
branchSplitFromStabilityLabels Man page Source code
branchSplitFromStabilityLabels.individualFraction Man page Source code
branchSplitFromStabilityLabels.prediction Man page Source code
checkAdjMat Man page Source code
checkSets Man page Source code
checkSimilarity Man page Source code
chooseOneHubInEachModule Man page Source code
chooseTopHubInEachModule Man page Source code
clusterCoef Man page Source code
coClustering Man page Source code
coClustering.permutationTest Man page Source code
colQuantileC Man page Source code
collapseRows Man page Source code
collapseRowsUsingKME Man page
collectGarbage Man page Source code
conformityBasedNetworkConcepts Man page Source code
conformityDecomposition Man page
consensusCalculation Man page Source code
consensusDissTOMandTree Man page
consensusKME Man page Source code
consensusMEDissimilarity Man page Source code
consensusOrderMEs Man page Source code
consensusProjectiveKMeans Man page
consensusRepresentatives Man page Source code
consensusTOM Man page Source code
consensusTreeInputs Man page Source code
convertNumericColumnsToNumeric Man page Source code
cor Man page Source code
cor1 Man page Source code
corAndPvalue Man page Source code
corFast Man page Source code
corPredictionSuccess Man page Source code
corPvalueFisher Man page Source code
corPvalueStudent Man page Source code
correlationPreservation Man page Source code
coxRegressionResiduals Man page Source code
cutreeStatic Man page Source code
cutreeStaticColor Man page Source code
disableWGCNAThreads Man page Source code
displayColors Man page Source code
dynamicMergeCut Man page Source code
empiricalBayesLM Man page Source code
enableWGCNAThreads Man page Source code
exportNetworkToCytoscape Man page Source code
exportNetworkToVisANT Man page Source code
factorizeNonNumericColumns Man page Source code
fixDataStructure Man page Source code
formatLabels Man page Source code
fundamentalNetworkConcepts Man page Source code
goodGenes Man page Source code
goodGenesMS Man page Source code
goodSamples Man page Source code
goodSamplesGenes Man page Source code
goodSamplesGenesMS Man page Source code
goodSamplesMS Man page Source code
greenBlackRed Man page Source code
greenWhiteRed Man page Source code
hierarchicalBranchEigengeneDissim Man page Source code
hierarchicalConsensusCalculation Man page Source code
hierarchicalConsensusKME Man page Source code
hierarchicalConsensusMEDissimilarity Man page Source code
hierarchicalConsensusModules Man page Source code
hierarchicalConsensusTOM Man page Source code
hierarchicalMergeCloseModules Man page Source code
hubGeneSignificance Man page Source code
imputeByModule Man page Source code
individualTOMs Man page Source code
initProgInd Man page Source code
intramodularConnectivity Man page Source code
intramodularConnectivity.fromExpr Man page Source code
isMultiData Man page Source code
kMEcomparisonScatterplot Man page
keepCommonProbes Man page Source code
labelPoints Man page Source code
labeledBarplot Man page
labeledHeatmap Man page
labeledHeatmap.multiPage Man page Source code
labels2colors Man page Source code
list2multiData Man page Source code
lowerTri2matrix Man page Source code
matchLabels Man page Source code
matrixToNetwork Man page Source code
mergeBlockwiseData Man page Source code
mergeCloseModules Man page Source code
metaAnalysis Man page Source code
metaZfunction Man page Source code
minWhichMin Man page Source code
modifiedBisquareWeights Man page Source code
moduleColor.getMEprefix Man page Source code
moduleEigengenes Man page Source code
moduleMergeUsingKME Man page
moduleNumber Man page Source code
modulePreservation Man page Source code
mtd.apply Man page Source code
mtd.applyToSubset Man page Source code
mtd.branchEigengeneDissim Man page Source code
mtd.colnames Man page Source code
mtd.mapply Man page Source code
mtd.rbindSelf Man page Source code
mtd.setAttr Man page Source code
mtd.setColnames Man page Source code
mtd.simplify Man page Source code
mtd.subset Man page Source code
multiData Man page Source code
multiData.eigengeneSignificance Man page Source code
multiData2list Man page Source code
multiGSub Man page Source code
multiGrep Man page Source code
multiGrepl Man page Source code
multiIntersect Man page Source code
multiSetMEs Man page Source code
multiSub Man page Source code
multiUnion Man page Source code
mutualInfoAdjacency Man page Source code
nPresent Man page Source code
nSets Man page Source code
nearestCentroidPredictor Man page Source code
nearestNeighborConnectivity Man page Source code
nearestNeighborConnectivityMS Man page Source code
networkConcepts Man page Source code
networkScreening Man page Source code
networkScreeningGS Man page Source code
newBlockInformation Man page Source code
newBlockwiseData Man page Source code
newConsensusOptions Man page Source code
newConsensusTree Man page Source code
newCorrelationOptions Man page Source code
newNetworkOptions Man page Source code
normalizeLabels Man page Source code
numbers2colors Man page Source code
orderBranchesUsingHubGenes Man page Source code
orderMEs Man page Source code
orderMEsByHierarchicalConsensus Man page Source code
overlapTable Man page Source code
overlapTableUsingKME Man page Source code
pickHardThreshold Man page
pickHardThreshold.fromSimilarity Man page
pickSoftThreshold Man page
pickSoftThreshold.fromSimilarity Man page
plotClusterTreeSamples Man page Source code
plotColorUnderTree Man page Source code
plotCor Man page Source code
plotDendroAndColors Man page Source code
plotEigengeneNetworks Man page Source code
plotMEpairs Man page Source code
plotMat Man page Source code
plotModuleSignificance Man page Source code
plotMultiHist Man page Source code
plotNetworkHeatmap Man page Source code
plotOrderedColors Man page Source code
pmean Man page Source code
pmean.fromList Man page Source code
pmedian Man page Source code
pminWhich.fromList Man page Source code
populationMeansInAdmixture Man page
pquantile Man page Source code
pquantile.fromList Man page Source code
prepComma Man page Source code
prependZeros Man page Source code
prependZeros.int Man page Source code
preservationNetworkConnectivity Man page Source code
projectiveKMeans Man page
propVarExplained Man page Source code
proportionsInAdmixture Man page
pruneAndMergeConsensusModules Man page Source code
pruneConsensusModules Man page Source code
qvalue Man page Source code
qvalue.restricted Man page Source code
randIndex Man page Source code
rankPvalue Man page Source code
recutBlockwiseTrees Man page Source code
recutConsensusTrees Man page Source code
redWhiteGreen Man page Source code
reflectBranch Man page
relativeCorPredictionSuccess Man page Source code
removeGreyME Man page Source code
removePrincipalComponents Man page Source code
replaceMissing Man page Source code
returnGeneSetsAsList Man page
rgcolors.func Man page Source code
rowQuantileC Man page Source code
sampledBlockwiseModules Man page Source code
sampledHierarchicalConsensusModules Man page Source code
scaleFreeFitIndex Man page Source code
scaleFreePlot Man page Source code
selectBranch Man page
selectFewestConsensusMissing Man page Source code
setCorrelationPreservation Man page Source code
shortenStrings Man page Source code
sigmoidAdjacencyFunction Man page Source code
signedKME Man page Source code
signifNumeric Man page Source code
signumAdjacencyFunction Man page Source code
simpleConsensusCalculation Man page Source code
simpleHierarchicalConsensusCalculation Man page Source code
simulateDatExpr Man page Source code
simulateDatExpr5Modules Man page Source code
simulateEigengeneNetwork Man page Source code
simulateModule Man page Source code
simulateMultiExpr Man page Source code
simulateSmallLayer Man page Source code
sizeGrWindow Man page Source code
sizeRestrictedClusterMerge Man page Source code
softConnectivity Man page Source code
softConnectivity.fromSimilarity Man page Source code
spaste Man page Source code
standardColors Man page Source code
standardScreeningBinaryTrait Man page Source code
standardScreeningCensoredTime Man page
standardScreeningNumericTrait Man page
stdErr Man page Source code
stratifiedBarplot Man page
subsetTOM Man page Source code
swapTwoBranches Man page
transposeBigData Man page
unsignedAdjacency Man page Source code
updateProgInd Man page Source code
userListEnrichment Man page
vectorTOM Man page Source code
vectorizeMatrix Man page Source code
verboseBarplot Man page
verboseBoxplot Man page Source code
verboseIplot Man page
verboseScatterplot Man page Source code
votingLinearPredictor Man page Source code
WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.

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