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WGCNA  

Weighted Correlation Network Analysis
View on CRAN: Click here


Download and install WGCNA package within the R console
Install from CRAN:
install.packages("WGCNA")

Install from Github:
library("remotes")
install_github("cran/WGCNA")

Install by package version:
library("remotes")
install_version("WGCNA", "1.72-5")



Attach the package and use:
library("WGCNA")
Maintained by
Peter Langfelder
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2010-07-26
Latest Update: 2023-01-18
Description:
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
How to cite:
Peter Langfelder (2010). WGCNA: Weighted Correlation Network Analysis. R package version 1.72-5, https://cran.r-project.org/web/packages/WGCNA
Previous versions and publish date:
0.92-3 (2010-07-26 19:08), 0.93 (2010-08-26 08:43), 0.94 (2010-09-08 09:59), 0.95 (2010-09-17 11:52), 0.96 (2010-09-23 08:14), 0.97 (2010-11-03 08:37), 0.98 (2010-11-13 16:19), 0.99 (2010-12-22 09:58), 1.00 (2011-02-15 10:52), 1.10-2 (2011-04-24 12:30), 1.11-1 (2011-06-01 06:32), 1.11-2 (2011-06-06 21:31), 1.11-3 (2011-07-07 10:07), 1.11 (2011-05-13 08:58), 1.12 (2011-08-17 07:30), 1.13 (2011-08-18 07:33), 1.14 (2011-11-10 13:59), 1.15 (2011-11-12 17:15), 1.17 (2011-12-07 11:13), 1.18-1 (2012-01-05 02:39), 1.18-2 (2012-01-13 09:05), 1.18 (2011-12-24 13:10), 1.19 (2012-03-03 08:10), 1.20 (2012-04-24 05:59), 1.22 (2012-06-19 08:33), 1.23-1 (2012-08-03 07:13), 1.25-1 (2012-11-09 21:25), 1.25-2 (2012-12-02 08:07), 1.25 (2012-11-09 04:10), 1.26 (2013-03-07 08:00), 1.27-1 (2013-04-02 07:29), 1.34 (2013-10-10 20:23), 1.41-1 (2014-06-14 07:29), 1.42 (2014-12-04 20:57), 1.43 (2015-01-15 21:06), 1.46 (2015-03-28 08:42), 1.47 (2015-06-16 00:57), 1.48 (2015-10-30 00:59), 1.49 (2015-12-29 08:22), 1.51 (2016-03-15 00:24), 1.60 (2017-07-10 07:28), 1.61 (2017-08-05 12:30), 1.62 (2018-02-13 00:11), 1.63 (2018-02-27 19:01), 1.64-1 (2018-09-11 10:20), 1.66 (2018-10-24 11:30), 1.67 (2019-04-11 20:52), 1.68 (2019-05-23 07:10), 1.69 (2020-02-28 20:00), 1.70-3 (2021-02-28 21:20), 1.71 (2022-04-23 00:00), 1.72-1 (2023-01-18 13:10)
Other packages that cited WGCNA R package
View WGCNA citation profile
Other R packages that WGCNA depends, imports, suggests or enhances
Functions, R codes and Examples using the WGCNA R package
Some associated functions: AFcorMI . BD.getData . BloodLists . BrainLists . BrainRegionMarkers . GOenrichmentAnalysis . GTOMdist . ImmunePathwayLists . PWLists . SCsLists . TOMplot . TOMsimilarity . TOMsimilarityFromExpr . TrueTrait . accuracyMeasures . addErrorBars . addGrid . addGuideLines . addTraitToMEs . adjacency . adjacency.polyReg . adjacency.splineReg . alignExpr . allocateJobs . allowWGCNAThreads . automaticNetworkScreening . automaticNetworkScreeningGS . bicor . bicorAndPvalue . bicovWeights . binarizeCategoricalColumns . binarizeCategoricalVariable . blockSize . blockwiseConsensusModules . blockwiseIndividualTOMs . blockwiseModules . blueWhiteRed . branchEigengeneDissim . branchSplit.dissim . branchSplit . branchSplitFromStabilityLabels . checkAdjMat . checkSets . chooseOneHubInEachModule . chooseTopHubInEachModule . clusterCoef . coClustering . coClustering.permutationTest . colQuantileC . collapseRows . collapseRowsUsingKME . collectGarbage . conformityBasedNetworkConcepts . conformityDecomposition . consensusCalculation . consensusDissTOMandTree . consensusKME . consensusMEDissimilarity . consensusOrderMEs . consensusProjectiveKMeans . consensusRepresentatives . consensusTOM . consensusTreeInputs . convertNumericColumnsToNumeric . cor . corAndPvalue . corPredictionSuccess . corPvalueFisher . corPvalueStudent . correlationPreservation . coxRegressionResiduals . cutreeStatic . cutreeStaticColor . displayColors . dynamicMergeCut . empiricalBayesLM . exportNetworkToCytoscape . exportNetworkToVisANT . factorizeNonNumericColumns . fixDataStructure . formatLabels . fundamentalNetworkConcepts . goodGenes . goodGenesMS . goodSamples . goodSamplesGenes . goodSamplesGenesMS . goodSamplesMS . greenBlackRed . greenWhiteRed . hierarchicalConsensusCalculation . hierarchicalConsensusKME . hierarchicalConsensusMEDissimilarity . hierarchicalConsensusModules . hierarchicalConsensusTOM . hierarchicalMergeCloseModules . hubGeneSignificance . imputeByModule . individualTOMs . initProgInd . intramodularConnectivity . isMultiData . kMEcomparisonScatterplot . keepCommonProbes . labelPoints . labeledBarplot . labeledHeatmap.multiPage . labeledHeatmap . labels2colors . list2multiData . lowerTri2matrix . matchLabels . matrixToNetwork . mergeCloseModules . metaAnalysis . metaZfunction . minWhichMin . moduleColor.getMEprefix . moduleEigengenes . moduleMergeUsingKME . moduleNumber . modulePreservation . mtd.apply . mtd.mapply . mtd.rbindSelf . mtd.setAttr . mtd.setColnames . mtd.simplify . mtd.subset . multiData.eigengeneSignificance . multiData . multiGSub . multiSetMEs . multiUnion . mutualInfoAdjacency . nPresent . nSets . nearestCentroidPredictor . nearestNeighborConnectivity . nearestNeighborConnectivityMS . networkConcepts . networkScreening . networkScreeningGS . newBlockInformation . newBlockwiseData . newConsensusOptions . newConsensusTree . newCorrelationOptions . newNetworkOptions . normalizeLabels . numbers2colors . orderBranchesUsingHubGenes . orderMEs . orderMEsByHierarchicalConsensus . overlapTable . overlapTableUsingKME . pickHardThreshold . pickSoftThreshold . plotClusterTreeSamples . plotColorUnderTree . plotCor . plotDendroAndColors . plotEigengeneNetworks . plotMEpairs . plotMat . plotModuleSignificance . plotMultiHist . plotNetworkHeatmap . populationMeansInAdmixture . pquantile . prepComma . prependZeros . preservationNetworkConnectivity . projectiveKMeans . propVarExplained . proportionsInAdmixture . pruneAndMergeConsensusModules . pruneConsensusModules . qvalue . qvalue.restricted . randIndex . rankPvalue . recutBlockwiseTrees . recutConsensusTrees . redWhiteGreen . relativeCorPredictionSuccess . removeGreyME . removePrincipalComponents . replaceMissing . returnGeneSetsAsList . rgcolors.func . sampledBlockwiseModules . sampledHierarchicalConsensusModules . scaleFreeFitIndex . scaleFreePlot . selectFewestConsensusMissing . setCorrelationPreservation . shortenStrings . sigmoidAdjacencyFunction . signedKME . signifNumeric . signumAdjacencyFunction . simpleConsensusCalculation . simpleHierarchicalConsensusCalculation . simulateDatExpr . simulateDatExpr5Modules . simulateEigengeneNetwork . simulateModule . simulateMultiExpr . simulateSmallLayer . sizeGrWindow . sizeRestrictedClusterMerge . softConnectivity . spaste . standardColors . standardScreeningBinaryTrait . standardScreeningCensoredTime . standardScreeningNumericTrait . stdErr . stratifiedBarplot . subsetTOM . swapTwoBranches . transposeBigData . unsignedAdjacency . userListEnrichment . vectorTOM . vectorizeMatrix . verboseBarplot . verboseBoxplot . verboseIplot . verboseScatterplot . votingLinearPredictor . 
Some associated R codes: AFcorMI.R . Functions-fromSimilarity.R . Functions-multiData.R . Functions.R . GOenrichmentAnalysis.R . TrueTrait.R . accuracyMeasures.R . adjacency.polyReg.R . adjacency.splineReg.R . blockwiseData.R . blockwiseModulesC.R . branchSplit.R . coClustering.R . collapseRows.R . collapseRowsUsingKME.R . conformityDecomposition.R . consensusCalculations.R . consensusDissTOMandTree.R . consensusRepresentatives.R . consensusTOM.R . corAndPvalue.R . corFunctions.R . coxRegressionResiduals.R . dendrogramAdjustmentFunctions.R . empiricalBayesLM.R . exportFunctions.R . heatmapWithLegend.R . hierarchicalConsensusModules.R . internalConstants.R . kMEcomparisonScatterplot.R . labelPoints.R . labeledHeatmap.R . matchLabels.R . moduleMergeUsingKME.R . modulePreservation.R . multiData.R . mutualInfoAdjacency.R . nearestCentroidPredictor.R . networkConcepts.R . overlapTableUsingKME.R . plotDendrogram.R . populationMeansInAdmixture.R . proportionsInAdmixture.R . quantileC.R . qvalue.R . returnGeneSetsAsList.R . sampledModules.R . smaFunctions.R . standardScreeningBinaryTrait.R . stratifiedBarplot.R . transposeBigData.R . useNThreads.R . userListEnrichment.R . verboseIplot.R . votingLinearPredictor.R . zzz.R .  Full WGCNA package functions and examples
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