Package 'WGCNA' - UCLA Human Genetics

WGCNA-package 7cutreeStaticColor Constant height tree cut using color labelsdisplayColorsShow colors used to label modulesdynamicMergeCutThreshold for module mergingexportNetworkToVisANT Export network data in format readable by VisANTexportNetworkToCytoscapeExport network data in format readable by CytoscapefixDataStructure Put single-set data into a form useful for multiset calcfundamentalNetworkConceptsCalculation of fundamental network conceptsGOenrichmentAnalysis Calculate enrichment p-values of clusters in GO termsgoodGenesFilter genes with too many missing entriesgoodGenesMSFilter genes with too many missing entries across multipgoodSamplesFilter samples with too many missing entriesgoodSamplesGenes Iterative filtering of samples and genes withtoo many missing entriesgoodSamplesGenesMS Iterative filtering of samples and genes with too many mmultiple data setsgoodSamplesMSFilter samples with too many missing entries across multgreenBlackRedGreen-black-red color sequencegreenWhiteRedGreen-white-red color sequencehubGeneSignificance Hubgene significanceinitProgIndInline display of progressintramodularConnectivityCalculation of intramodular connectivitykeepCommonProbes Keep probes that are shared among given data setskMEcomparisonScatterplotScatterplots of eigengene-based connectivitylabeledBarplotBarplot with text or color labelslabeledHeatmapProduce a labeled heatmap plotlabelPoints Attempt to intelligently label points in a scatterplotlabels2colorsConvert numerical labels to colorslowerTri2matrixReconstruct a symmetric matrix from a distance(lower-triangular) representationmatchLabelsRelabel modules to best approximate a reference labelingmergeCloseModules Merge close modules in gene expression datametaAnalysisMeta-analysis significance statisticsmetaZfunctionMeta-analysis Z statisticmoduleColor.getMEprefixGet the prefix used to label module eigengenesmoduleEigengenes Calculate module eigengenesmoduleMergeUsingKME Merge modules and reassign genes using kMEmoduleNumberFixed-height cut of a dendrogrammodulePreservation Calculation of module preservation statisticsmultiSetMEsCalculate module eigengenesmultiData.eigengeneSignificanceCalculate eigengene significance for multiple data setsmutualInfoAdjacency Calculate weighted adjacency matrices based on mutual innPresentNumber of present data entriesnearestNeighborConnectivityConnectivity to a constant number of nearest neighborsnearestNeighborConnectivityMSConnectivity to a constant number of nearest