WGCNAplus/NAMESPACE at main · bigomics/WGCNAplus · GitHub

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# Generated by roxygen2: do not edit by hand

export(ai.ask)
export(ai.ask_ellmer)
export(ai.ask_tidyprompt)
export(ai.create_image_gemini)
export(ai.create_image_grok)
export(ai.create_image_openai)
export(ai.get_ollama_models)
export(calculateCompoundSignificance)
export(cbind_sparse_matrix)
export(checkDendroHeights)
export(collapseTraitMatrix)
export(computeConsensusGeneStats)
export(computeConsensusMatrix)
export(computeConsensusModuleEnrichment)
export(computeGeneStats)
export(computeModuleEnrichment)
export(computeModules)
export(computeWGCNA)
export(computeWGCNA_multiomics)
export(cor_sparse_matrix)
export(corpora.fastFET)
export(cortest)
export(createConsensusLayers)
export(create_diagram)
export(create_infographic)
export(create_module_infographic)
export(create_report)
export(describeModules)
export(dot.rankdir)
export(expandPhenoMatrix)
export(fastTOMsimilarity)
export(getConsensusGeneStats)
export(getGeneStats)
export(getModuleCrossGenes)
export(getPlaydataGMT)
export(getTopGenesAndSets)
export(getTopModules)
export(getTopTables)
export(get_modTraits)
export(graph2dot)
export(gset.fastFET)
export(gset.fisher)
export(gset.fisherLIST)
export(gset.rankcor)
export(gx.limma)
export(imputeMissing)
export(is.Date)
export(labels2colors)
export(logCPM)
export(makeContrastsFromLabelMatrix)
export(mat2gmt)
export(matchColors)
export(mergeCloseModules)
export(merge_block_dendrograms)
export(merge_sparse_matrix)
export(mofa.get_prefix)
export(mofa.merge_data)
export(mofa.merge_data2)
export(mofa.prefix)
export(mofa.split_data)
export(mofa.strip_prefix)
export(mofa.topSD)
export(pgx.supercell)
export(pickSoftThreshold)
export(plotConsensusOverlapHeatmap)
export(plotConsensusSampleDendroAndColors)
export(plotConsensusTraitCorrelation)
export(plotDendroAndColors)
export(plotEigenGeneAdjacencyHeatmap)
export(plotEigenGeneClusterDendrogram)
export(plotEigenGeneGraph)
export(plotFeatureUMAP)
export(plotGeneNetwork)
export(plotLabeledCorrelationHeatmap)
export(plotMDS)
export(plotModuleHeatmap)
export(plotModuleHubGenes)
export(plotModuleScores)
export(plotModuleScores.BAK)
export(plotModuleSignificance)
export(plotModuleTraitHeatmap)
export(plotMultiDendroAndColors)
export(plotMultiEigengeneCorrelation)
export(plotPowerAnalysis)
export(plotPreservationModuleTraits)
export(plotPreservationSummaries)
export(plotSampleDendroAndColors)
export(plotTOM)
export(plotTraitCorrelationBarPlots)
export(probe2symbol)
export(purpleGreyYellow)
export(rename_by2)
export(rho2bluered)
export(rowmean)
export(runConsensusWGCNA)
export(runPreservationWGCNA)
export(svdImpute2)
export(tidy.dataframe)
export(wgcna.plot_lasagna)
import(WGCNA)
importFrom(Matrix,crossprod)
importFrom(Matrix,t)
importFrom(dynamicTreeCut,cutreeDynamic)
importFrom(fastcluster,hclust)
importFrom(fgsea,fgsea)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,hcl.colors)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,box)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(irlba,irlba)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,colSds)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowSds)
importFrom(methods,is)
importFrom(stats,as.dist)
importFrom(stats,cor.test)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(utils,type.convert)