Files in WGCNA

Weighted Correlation Network Analysis

R/votingLinearPredictor.R R/proportionsInAdmixture.R R/userListEnrichment.R R/quantileC.R R/accuracyMeasures.R R/heatmapWithLegend.R R/AFcorMI.R R/blockwiseData.R R/collapseRows.R R/networkConcepts.R R/verboseIplot.R R/consensusCalculations.R R/mutualInfoAdjacency.R R/corAndPvalue.R R/transposeBigData.R R/adjacency.polyReg.R R/conformityDecomposition.R R/corFunctions.R R/plotDendrogram.R R/labelPoints.R R/returnGeneSetsAsList.R R/GOenrichmentAnalysis.R R/smaFunctions.R R/nearestCentroidPredictor.R R/moduleMergeUsingKME.R R/Functions-fromSimilarity.R R/qvalue.R R/coClustering.R R/standardScreeningBinaryTrait.R R/multiData.R R/matchLabels.R R/consensusDissTOMandTree.R R/kMEcomparisonScatterplot.R R/collapseRowsUsingKME.R R/coxRegressionResiduals.R R/overlapTableUsingKME.R R/internalConstants.R R/exportFunctions.R R/dendrogramAdjustmentFunctions.R R/Functions-multiData.R R/empiricalBayesLM.R R/Functions.R R/zzz.R R/hierarchicalConsensusModules.R R/adjacency.splineReg.R R/populationMeansInAdmixture.R R/modulePreservation.R R/blockwiseModulesC.R R/TrueTrait.R R/stratifiedBarplot.R R/consensusTOM.R R/sampledModules.R R/labeledHeatmap.R R/branchSplit.R R/consensusRepresentatives.R R/useNThreads.R man/goodSamplesMS.Rd man/mtd.rbindSelf.Rd man/normalizeLabels.Rd man/AFcorMI.Rd man/metaZfunction.Rd man/multiData.Rd man/bicorAndPvalue.Rd man/factorizeNonNumericColumns.Rd man/fixDataStructure.Rd man/plotMultiHist.Rd man/standardColors.Rd man/addTraitToMEs.Rd man/labeledHeatmap.Rd man/pruneAndMergeConsensusModules.Rd man/isMultiData.Rd man/overlapTableUsingKME.Rd man/standardScreeningNumericTrait.Rd man/numbers2colors.Rd man/hierarchicalConsensusModules.Rd man/mtd.simplify.Rd man/plotClusterTreeSamples.Rd man/scaleFreePlot.Rd man/consensusDissTOMandTree.Rd man/newBlockwiseData.Rd man/rankPvalue.Rd man/automaticNetworkScreening.Rd man/standardScreeningBinaryTrait.Rd man/multiData.eigengeneSignificance.Rd man/plotNetworkHeatmap.Rd man/consensusTreeInputs.Rd man/standardScreeningCensoredTime.Rd man/individualTOMs.Rd man/sizeGrWindow.Rd man/prepComma.Rd man/nearestCentroidPredictor.Rd man/nearestNeighborConnectivityMS.Rd man/matchLabels.Rd man/plotColorUnderTree.Rd man/consensusCalculation.Rd man/displayColors.Rd man/selectFewestConsensusMissing.Rd man/swapTwoBranches.Rd man/mtd.setAttr.Rd man/removePrincipalComponents.Rd man/simpleHierarchicalConsensusCalculation.Rd man/BD.getData.Rd man/automaticNetworkScreeningGS.Rd man/colQuantileC.Rd man/networkScreeningGS.Rd man/hierarchicalConsensusTOM.Rd man/list2multiData.Rd man/metaAnalysis.Rd man/GTOMdist.Rd man/collapseRowsUsingKME.Rd man/clusterCoef.Rd man/bicovWeights.Rd man/consensusOrderMEs.Rd man/minWhichMin.Rd man/setCorrelationPreservation.Rd man/coClustering.Rd man/userListEnrichment.Rd man/BloodLists.Rd man/orderMEs.Rd man/shortenStrings.Rd man/corPvalueFisher.Rd man/cutreeStatic.Rd man/initProgInd.Rd man/nearestNeighborConnectivity.Rd man/kMEcomparisonScatterplot.Rd man/checkSets.Rd man/overlapTable.Rd man/networkScreening.Rd man/recutBlockwiseTrees.Rd man/prependZeros.Rd man/removeGreyME.Rd man/simulateMultiExpr.Rd man/allocateJobs.Rd man/multiUnion.Rd man/nPresent.Rd man/hierarchicalConsensusMEDissimilarity.Rd man/randIndex.Rd man/consensusProjectiveKMeans.Rd man/corPredictionSuccess.Rd man/simpleConsensusCalculation.Rd man/TOMsimilarity.Rd man/TrueTrait.Rd man/blockwiseConsensusModules.Rd man/moduleEigengenes.Rd man/verboseBarplot.Rd man/pruneConsensusModules.Rd man/corAndPvalue.Rd man/adjacency.polyReg.Rd man/sampledBlockwiseModules.Rd man/relativeCorPredictionSuccess.Rd man/PWLists.Rd man/mtd.apply.Rd man/pickHardThreshold.Rd man/verboseIplot.Rd man/nSets.Rd man/collectGarbage.Rd man/projectiveKMeans.Rd man/allowWGCNAThreads.Rd man/hubGeneSignificance.Rd man/exportNetworkToCytoscape.Rd man/goodSamples.Rd man/labels2colors.Rd man/multiSetMEs.Rd man/recutConsensusTrees.Rd man/SCsLists.Rd man/empiricalBayesLM.Rd man/intramodularConnectivity.Rd man/addErrorBars.Rd man/orderMEsByHierarchicalConsensus.Rd man/plotEigengeneNetworks.Rd man/unsignedAdjacency.Rd man/softConnectivity.Rd man/verboseScatterplot.Rd man/scaleFreeFitIndex.Rd man/consensusRepresentatives.Rd man/formatLabels.Rd man/mutualInfoAdjacency.Rd man/alignExpr.Rd man/keepCommonProbes.Rd man/signifNumeric.Rd man/plotMat.Rd man/pickSoftThreshold.Rd man/orderBranchesUsingHubGenes.Rd man/goodGenesMS.Rd man/matrixToNetwork.Rd man/redWhiteGreen.Rd man/propVarExplained.Rd man/rgcolors.func.Rd man/mtd.mapply.Rd man/addGuideLines.Rd man/lowerTri2matrix.Rd man/accuracyMeasures.Rd man/branchSplit.Rd man/simulateDatExpr5Modules.Rd man/binarizeCategoricalVariable.Rd man/vectorizeMatrix.Rd man/simulateEigengeneNetwork.Rd man/sizeRestrictedClusterMerge.Rd man/sigmoidAdjacencyFunction.Rd man/goodSamplesGenesMS.Rd man/plotCor.Rd man/simulateModule.Rd man/labeledBarplot.Rd man/preservationNetworkConnectivity.Rd man/newCorrelationOptions.Rd man/newConsensusOptions.Rd man/proportionsInAdmixture.Rd man/plotModuleSignificance.Rd man/fundamentalNetworkConcepts.Rd man/BrainRegionMarkers.Rd man/replaceMissing.Rd man/multiGSub.Rd man/cutreeStaticColor.Rd man/modulePreservation.Rd man/labeledHeatmap.multiPage.Rd man/signumAdjacencyFunction.Rd man/vectorTOM.Rd man/moduleColor.getMEprefix.Rd man/convertNumericColumnsToNumeric.Rd man/newBlockInformation.Rd man/coClustering.permutationTest.Rd man/branchEigengeneDissim.Rd man/qvalue.restricted.Rd man/blockwiseModules.Rd man/spaste.Rd man/exportNetworkToVisANT.Rd man/stratifiedBarplot.Rd man/collapseRows.Rd man/adjacency.splineReg.Rd man/moduleMergeUsingKME.Rd man/moduleNumber.Rd man/votingLinearPredictor.Rd man/GOenrichmentAnalysis.Rd man/stdErr.Rd man/adjacency.Rd man/simulateDatExpr.Rd man/BrainLists.Rd man/checkAdjMat.Rd man/corPvalueStudent.Rd man/dynamicMergeCut.Rd man/populationMeansInAdmixture.Rd man/verboseBoxplot.Rd man/plotMEpairs.Rd man/hierarchicalConsensusKME.Rd man/addGrid.Rd man/chooseTopHubInEachModule.Rd man/consensusMEDissimilarity.Rd man/TOMplot.Rd man/blockSize.Rd man/conformityBasedNetworkConcepts.Rd man/simulateSmallLayer.Rd man/modifiedBisquareWeights.Rd man/conformityDecomposition.Rd man/hierarchicalMergeCloseModules.Rd man/branchSplit.dissim.Rd man/imputeByModule.Rd man/hierarchicalConsensusCalculation.Rd man/bicor.Rd man/blockwiseIndividualTOMs.Rd man/subsetTOM.Rd man/qvalue.Rd man/newConsensusTree.Rd man/sampledHierarchicalConsensusModules.Rd man/branchSplitFromStabilityLabels.Rd man/mergeCloseModules.Rd man/consensusTOM.Rd man/signedKME.Rd man/greenWhiteRed.Rd man/pquantile.Rd man/blueWhiteRed.Rd man/consensusKME.Rd man/networkConcepts.Rd man/cor.Rd man/mtd.setColnames.Rd man/greenBlackRed.Rd man/mtd.subset.Rd man/labelPoints.Rd man/coxRegressionResiduals.Rd man/ImmunePathwayLists.Rd man/plotDendroAndColors.Rd man/returnGeneSetsAsList.Rd man/TOMsimilarityFromExpr.Rd man/correlationPreservation.Rd man/goodSamplesGenes.Rd man/goodGenes.Rd man/transposeBigData.Rd man/newNetworkOptions.Rd man/chooseOneHubInEachModule.Rd man/binarizeCategoricalColumns.Rd