_pkgdown.yml

title: hdWGCNA

url: https://smorabit.github.io/hdWGCNA/

template:
  bootstrap: 5
  bootswatch: flatly

home:
  title: hdWGCNA
  sidebar:
    structure: [license, citation, authors, dev]

authors:
  Sam Morabito:
    href: https://smorabit.github.io
  Zechuan Shi:
    href: https://github.com/rootze
  Swarup Lab:
    href: https://swaruplab.bio.uci.edu/

navbar:
  structure:
    left: [intro, articles, reference, news]
    right: [search, github]
  components:
   intro:
     text: Get started
     href: articles/basic_tutorial.html
   news:
     text: News
     href: news/index.html
   articles:
    text: Vignettes
    menu:
    - text: Core functionality
    - text: hdWGCNA in single-cell data
      href: articles/basic_tutorial.html
    - text: hdWGCNA in spatial transcriptomics data
      href: articles/ST_basics.html
    - text: Isoform co-expression network analysis with PacBio MAS-Seq
      href: articles/isoform_pbmcs.html
    - text: Network visualization
      href: articles/network_visualizations.html
    - text: -------
    - text: Biological context for co-expression modules
    - text: Differential module eigengene (DME) analysis
      href: articles/differential_MEs.html
    - text: Module trait correlation
      href: articles/module_trait_correlation.html
    - text: Enrichment analysis
      href: articles/enrichment_analysis.html
    - text: -------
    - text: Exploring modules in external datasets
    - text: Projecting modules to new datasets
      href: articles/projecting_modules.html
    - text: Module preservation and reproducibility
      href: articles/module_preservation.html
    - text: Cross-species and cross-modality analysis
      href: articles/projecting_modules_cross.html
    - text: -------
    - text: Advanced topics
    - text: Transcription factor regulatory network analysis
      href: articles/tf_network.html
    - text: Consensus network analysis
      href: articles/consensus_wgcna.html
    - text: hdWGCNA with pseudobulk data
      href: articles/pseudobulk.html
    - text: Co-expression module dynamics with pseudotime
      href: articles/pseudotime.html
    - text: -------
    - text: Other
    - text: Module customization
      href: articles/customization.html
    - text: Alternative metacell algorithms
      href: articles/other_metacells.html
    - text: Using SCTransform normalized data
      href: articles/sctransform.html
    - text: -------
    - text: All vignettes
      href: articles/index.html


reference:
- title: Data setup
  desc: Functions to set up the Seurat object for network analysis
  contents:
  - '`SetupForWGCNA`'
  - '`SelectNetworkGenes`'
  - '`FindMajorIsoforms`'
- title: Metacells and metaspots
  desc: Functions for constructing metacells from single-cell data and metaspots from ST data
  contents:
  - '`MetacellsByGroups`'
  - '`MetaspotsByGroups`'
- title: Network Analysis
  desc: Functions for constructing the co-expression network
  contents:
    - '`TestSoftPowers`'
    - '`TestSoftPowersConsensus`'
    - '`PlotSoftPowers`'
    - '`ConstructNetwork`'
    - '`ModuleEigengenes`'
    - '`ModuleConnectivity`'
- title: Network Visualization
  desc: Functions for visualizing the co-expression network
  contents:
    - '`PlotDendrogram`'
    - '`ModuleNetworkPlot`'
    - '`HubGeneNetworkPlot`'
    - '`RunModuleUMAP`'
    - '`ModuleUMAPPlot`'
- title: Differential analysis
  desc: Functions for differential module eigengene analysis
  contents:
    - '`FindDMEs`'
    - '`FindAllDMEs`'
    - '`PlotDMEsVolcano`'
    - '`PlotDMEsLollipop`'
- title: Enrichment Analysis
  desc: Functions for Enrichr analysis and DEG overlap analysis
  contents:
    - '`RunEnrichr`'
    - '`EnrichrBarPlot`'
    - '`EnrichrDotPlot`'
    - '`OverlapModulesDEGs`'
    - '`OverlapBarPlot`'
    - '`OverlapDotPlot`'
- title: Plotting
  desc: Functions for generating plots with hdWGCNA
  contents:
    - '`ModuleFeaturePlot`'
    - '`ModuleRadarPlot`'
    - '`PlotModuleTrajectory`'
- title: Transcription Factor Regulatory Networks
  contents:
    - '`MotifScan`'
    - '`ConstructTFNetwork`'
    - '`AssignTFRegulons`'
    - '`GetTFTargetGenes`'
    - '`TFNetworkPlot`'
    - '`RegulonScores`'
    - '`RegulonBarPlot`'
    - '`RunEnrichrRegulons`'
    - '`ModuleRegulatoryNetwork`'
    - '`ModuleRegulatoryNetworkPlot`'
    - '`ModuleRegulatoryHeatmap`'
    - '`FindDifferentialRegulons`'
    - '`PlotDifferentialRegulons`'
- title: Module Preservation
  desc: Functions for performing module preservation analysis
  contents:
    - '`ProjectModules`'
    - '`ModulePreservation`'
    - '`ModulePreservationNetRep`'
    - '`PlotModulePreservation`'
    - '`PlotModulePreservationLollipop`'
    - '`ModuleTopologyHeatmap`'
    - '`ModuleTopologyBarplot`'
- title: Module Trait Correlation
  desc: Functions for performing module trait correlation analysis
  contents:
    - '`ModuleTraitCorrelation`'
    - '`PlotModuleTraitCorrelation`'
- title: Transcription Factor Networks
  contents:
  - '`MotifScan`'
- title: Getters and setters
  desc: Functions to retrieve and set the values for various attributes
  contents:
    - '`SetActiveWGCNA`'
    - '`GetActiveWGCNA`'
    - '`SetMetacellObject`'
    - '`GetMetacellObject`'
    - '`SetWGCNAGenes`'
    - '`GetWGCNAGenes`'
    - '`SetDatExpr`'
    - '`GetDatExpr`'
    - '`SetMultiExpr`'
    - '`GetMultiExpr`'
    - '`SetWGCNAParams`'
    - '`GetWGCNAParams`'
    - '`SetPowerTable`'
    - '`GetPowerTable`'
    - '`SetNetworkData`'
    - '`GetNetworkData`'
    - '`SetModules`'
    - '`GetModules`'
    - '`GetHubGenes`'
    - '`SetMEs`'
    - '`GetMEs`'
    - '`SetMELoadings`'
    - '`GetMELoadings`'
    - '`SetEnrichrTable`'
    - '`GetEnrichrTable`'
    - '`SetModuleScores`'
    - '`GetModuleScores`'
    - '`GetTOM`'
    - '`SetModuleUMAP`'
    - '`GetModuleUMAP`'
    - '`SetModuleTraitCorrelation`'
    - '`GetModuleTraitCorrelation`'
    - '`SetModulePreservation`'
    - '`GetModulePreservation`'
    - '`SetMotifs`'
    - '`GetMotifs`'
    - '`SetMotifMatrix`'
    - '`GetMotifMatrix`'
    - '`SetPFMList`'
    - '`GetPFMList`'
    - '`SetMotifTargets`'
    - '`GetMotifTargets`'
    - '`SetMotifOverlap`'
    - '`GetMotifOverlap`'
    - '`SetMotifScores`'
    - '`GetMotifScores`'
    - '`SetDegrees`'
    - '`GetDegrees`'
    - '`GetTFRegulons`'
    - '`SetTFRegulons`'
    - '`GetTFEval`'
    - '`SetTFEval`'
    - '`GetRegulonScores`'
    - '`SetRegulonScores`'
    - '`GetEnrichrRegulonTable`'
    - '`SetEnrichrRegulonTable`'
    - '`GetMetacellParams`'
    - '`SetMetacellParams`'
    - '`SetTFNetwork`'
    - '`GetTFNetwork`'
- title: Seurat wrappers
  desc: Wrapper functions to run Seurat commands on the metacell data
  contents:
    - '`NormalizeMetacells`'
    - '`ScaleMetacells`'
    - '`RunPCAMetacells`'
    - '`RunHarmonyMetacells`'
    - '`RunUMAPMetacells`'
    - '`DimPlotMetacells`'
- title: Customization
  desc: Customization functions
  contents:
    - '`ResetModuleColors`'
    - '`ResetModuleNames`'
- title: Other
  desc: Other functions
  contents:
  - '`ConstructPseudobulk`'
  - '`ReassignModules`'
  - '`GetActiveWGCNAName`'
- title: internal
  contents:
  - umap_theme
  - to_pseudobulk
  - CheckSeurat5 
  - CheckWGCNAName
  - scale01 
  - shuffle_points
  - DoHubGeneHeatmap 
  - ConstructMetacells
  - ConstructMetaspots 
  - AvgModuleExpr 
  - ComputeModuleEigengene 
  - ModuleCorrNetwork 
  - ModuleCorrelogram 
  - ModuleExprScore 
  - OverlapModulesMotifs 
  - corSparse
  - check_inputs 
  - GetAvgModuleExpr
  - SetAvgModuleExpr
  - TransferModuleGenome 
  - PlotKMEs
  - PlotLollipop
  - BinPseudotime
  - MotifOverlapBarPlot

deploy:
  install_metadata: true