Package index • hdWGCNA

Data setup

Functions to set up the Seurat object for network analysis

SetupForWGCNA(): SetupForWGCNA

SelectNetworkGenes(): SelectNetworkGenes

FindMajorIsoforms(): FindMajorIsoforms

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

PlotDendrogram(): PlotDendrogram

ModuleNetworkPlot(): ModuleNetworkPlot

HubGeneNetworkPlot(): HubGeneNetworkPlot

RunModuleUMAP(): RunModuleUMAP

ModuleUMAPPlot(): ModuleUMAPPlot

Differential analysis

Functions for differential module eigengene analysis

FindDMEs(): FindDMEs

FindAllDMEs(): FindAllDMEs

PlotDMEsVolcano(): PlotDMEsVolcano

PlotDMEsLollipop(): PlotDMEsLollipop

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

ModuleRadarPlot(): ModuleRadarPlot

PlotModuleTrajectory(): PlotModuleTrajectory

Transcription Factor Regulatory Networks

MotifScan(): MotifScan

ConstructTFNetwork(): ConstructTFNetwork

AssignTFRegulons(): AssignTFRegulons

GetTFTargetGenes(): GetTFTargetGenes

TFNetworkPlot(): TFNetworkPlot

RegulonScores(): RegulonScores

RegulonBarPlot(): RegulonBarPlot

RunEnrichrRegulons(): RunEnrichrRegulons

ModuleRegulatoryNetwork(): ModuleRegulatoryNetwork

ModuleRegulatoryNetworkPlot(): ModuleRegulatoryNetworkPlot

ModuleRegulatoryHeatmap(): ModuleRegulatoryHeatmap

FindDifferentialRegulons(): FindDifferentialRegulons

PlotDifferentialRegulons(): PlotDifferentialRegulons

Module Preservation

Functions for performing module preservation analysis

ProjectModules(): ProjectModules

ModulePreservation(): ModulePreservation

ModulePreservationNetRep(): ModulePreservationNetRep

PlotModulePreservation(): PlotModulePreservation

PlotModulePreservationLollipop(): PlotModulePreservationLollipop

ModuleTopologyHeatmap(): ModuleTopologyHeatmap

ModuleTopologyBarplot(): ModuleTopologyBarplot

Module Trait Correlation

Functions for performing module trait correlation analysis

ModuleTraitCorrelation(): ModuleTraitCorrelation'

PlotModuleTraitCorrelation(): PlotModuleTraitCorrelation

Transcription Factor Networks

MotifScan(): MotifScan

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

SetDegrees(): SetDegrees

GetDegrees(): GetDegrees

GetTFRegulons(): GetTFRegulons

SetTFRegulons(): SetTFRegulons

GetTFEval(): GetTFEval

SetTFEval(): SetTFEval

GetRegulonScores(): GetRegulonScores

SetRegulonScores(): SetRegulonScores

GetEnrichrRegulonTable(): GetEnrichrRegulonTable

SetEnrichrRegulonTable(): SetEnrichRegulonTable

GetMetacellParams(): GetMetacellParams

SetMetacellParams(): SetMetacellParams

SetTFNetwork(): SetTFNetwork

GetTFNetwork(): GetTFNetwork

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

Other

Other functions

ConstructPseudobulk(): ConstructPseudobulk

ReassignModules(): ReassignModules

GetActiveWGCNAName(): GetActiveWGCNAName