Metacells and metaspots

Functions for constructing metacells from single-cell data and metaspots from ST data

MetacellsByGroups()

MetacellsByGroups

MetaspotsByGroups()

MetaspotsByGroups

Network Analysis

Functions for constructing the co-expression network

TestSoftPowers()

TestSoftPowers

TestSoftPowersConsensus()

TestSoftPowersConsensus

PlotSoftPowers()

PlotSoftPowers

ConstructNetwork()

ConstructNetwork

ModuleEigengenes()

ModuleEigengenes

ModuleConnectivity()

ModuleConnectivity

Network Visualization

Functions for visualizing the co-expression network

ModuleNetworkPlot()

ModuleNetworkPlot

HubGeneNetworkPlot()

HubGeneNetworkPlot

RunModuleUMAP()

RunModuleUMAP

ModuleUMAPPlot()

ModuleUMAPPlot

Differential analysis

Functions for differential module eigengene analysis

FindDMEs()

FindDMEs

FindAllDMEs()

FindAllDMEs

PlotDMEsVolcano()

PlotDMEsVolcano

Enrichment Analysis

Functions for Enrichr analysis and DEG overlap analysis

RunEnrichr()

RunEnrichr

EnrichrBarPlot()

EnrichrBarPlot

EnrichrDotPlot()

EnrichrDotPlot

OverlapModulesDEGs()

OverlapModulesDEGs

OverlapBarPlot()

OverlapBarPlot

OverlapDotPlot()

OverlapDotPlot

Plotting

Functions for generating plots with hdWGCNA

ModuleFeaturePlot()

ModuleFeaturePlot

Module Preservation

Functions for performing module preservation analysis

ModulePreservation()

ModulePreservation

PlotModulePreservation()

PlotModulePreservation

Module Trait Correlation

Functions for performing module trait correlation analysis

ModuleTraitCorrelation()

ModuleTraitCorrelation'

PlotModuleTraitCorrelation()

PlotModuleTraitCorrelation

Getters and setters

Functions to retrieve and set the values for various attributes

SetActiveWGCNA()

SetActiveWGCNA

GetActiveWGCNA()

GetActiveWGCNA

SetMetacellObject()

SetMetacellObject

GetMetacellObject()

GetMetacellObject

SetWGCNAGenes()

SetWGCNAGenes

GetWGCNAGenes()

GetWGCNAGenes

SetDatExpr()

SetDatExpr

GetDatExpr()

GetDatExpr

SetMultiExpr()

SetMultiExpr

GetMultiExpr()

GetMultiExpr

SetWGCNAParams()

SetWGCNAParams

GetWGCNAParams()

GetWGCNAParams

SetPowerTable()

SetPowerTable

GetPowerTable()

GetPowerTable

SetNetworkData()

SetNetworkData

GetNetworkData()

GetNetworkData

SetModules()

SetModules

GetModules()

GetModules

GetHubGenes()

GetHubGenes

SetMEs()

SetMEs

GetMEs()

GetMEs

SetMELoadings()

SetMELoadings

GetMELoadings()

GetMELoadings

SetEnrichrTable()

SetEnrichrTable

GetEnrichrTable()

GetEnrichrTable

SetModuleScores()

SetModuleScores

GetModuleScores()

GetModuleScores

GetTOM()

GetTOM

SetModuleUMAP()

SetModuleUMAP

GetModuleUMAP()

GetModuleUMAP

SetModuleTraitCorrelation()

SetModuleTraitCorrelation

GetModuleTraitCorrelation()

GetModuleTraitCorrelation

SetModulePreservation()

SetModulePreservation

GetModulePreservation()

GetModulePreservation

SetMotifs()

SetMotifs

GetMotifs()

GetMotifs

SetMotifMatrix()

SetMotifMatrix

GetMotifMatrix()

GetMotifMatrix

SetPFMList()

SetPFMList

GetPFMList()

GetPFMList

SetMotifTargets()

SetMotifTargets

GetMotifTargets()

GetMotifTargets

SetMotifOverlap()

SetMotifOverlap

GetMotifOverlap()

GetMotifOverlap

SetMotifScores()

SetMotifScores

GetMotifScores()

GetMotifScores

Seurat wrappers

Wrapper functions to run Seurat commands on the metacell data

NormalizeMetacells()

NormalizeMetacells

ScaleMetacells()

ScaleMetacells

RunPCAMetacells()

RunPCAMetacells

RunHarmonyMetacells()

RunHarmonyMetacells

RunUMAPMetacells()

RunUMAPMetacells

DimPlotMetacells()

DimPlotMetacells

Customization

Customization functions

ResetModuleColors()

ResetModuleColors

ResetModuleNames()

ResetModuleNames