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

NormalizeMetacells(): NormalizeMetacells

ScaleMetacells(): ScaleMetacells

RunPCAMetacells(): RunPCAMetacells

RunHarmonyMetacells(): RunHarmonyMetacells

RunUMAPMetacells(): RunUMAPMetacells

DimPlotMetacells(): DimPlotMetacells

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

ModuleCorrelogram(): ModuleCorrelogram

Differential Analysis

Functions for differential module eigengene analysis

FindDMEs(): FindDMEs

FindAllDMEs(): FindAllDMEs

PlotDMEsVolcano(): PlotDMEsVolcano

PlotDMEsLollipop(): PlotDMEsLollipop

Enrichment Analysis

Functions for Enrichr 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 Networks

Functions for TF regulatory network analysis

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

Customization

Customization functions

ResetModuleColors(): ResetModuleColors

ResetModuleNames(): ResetModuleNames

ReassignModules(): ReassignModules

Getters and Setters

Functions to retrieve and set values for various attributes

SetActiveWGCNA(): SetActiveWGCNA

GetActiveWGCNA(): GetActiveWGCNA

GetActiveWGCNAName(): GetActiveWGCNAName

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

SetAvgModuleExpr(): SetAvgModuleExpr

GetAvgModuleExpr(): GetAvgModuleExpr

Other Functions

Utility and miscellaneous functions

ConstructPseudobulk(): ConstructPseudobulk

CheckSeurat5(): CheckSeurat5

CheckWGCNAName(): CheckWGCNAName

TransferModuleGenome(): TransferModuleGenome

BinPseudotime(): BinPseudotime

Internal Functions

Internal helper functions (not typically called directly)

ConstructMetacells(): ConstructMetacells

ConstructMetaspots(): ConstructMetaspots

AvgModuleExpr(): AverageModuleExpr

ModuleExprScore(): ModuleExprScore

ModuleCorrNetwork(): ModuleCorrNetworks

OverlapModulesMotifs(): Overlap modules with TF target genes

corSparse(): Sparse matrix correlation

scale01(): scale01

shuffle_points(): shuffle_points

umap_theme(): umap_theme

DoHubGeneHeatmap(): Plots gene expression of hub genes as a heatmap

PlotKMEs(): PlotKMEs

MotifOverlapBarPlot(): Displays the top n TFs in a set of modules as a bar plot

ComputeModuleEigengene(): ComputeModuleEigengene

PlotLollipop(): PlotLollipop

check_inputs(): Check inputs

to_pseudobulk(): Create a pseudobulk matrix