Files in smorabit/hdWGCNA
hdWGCNA
.DS_Store
.github/ISSUE_TEMPLATE/bug-error-report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/question.md
.github/PULL_REQUEST_TEMPLATE/PULL_REQUEST_TEMPLATE.md
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/ConstructNetwork.R
R/ConstructTFNetwork.R
R/DMEs.R
R/Enrichment.R
R/FindMajorIsoforms.R
R/Metaspots.R
R/ModuleConnectivity.R
R/ModuleEigengenes.R
R/ModulePreservation.R
R/ModuleRegulatoryNetwork.R
R/ModuleTraitCorrelation.R
R/Motifs.R
R/ProjectModules.R
R/Pseudobulk.R
R/ReassignModules.R
R/RegulonBarPlot.R
R/Regulons.R
R/RunModuleUMAP.R
R/SelectNetworkGenes.R
R/SetupForWGCNA.R
R/SoftPowers.R
R/TFNetworkPlot.R
R/TF_functions.R
R/getters_and_setters.R
R/helpers.R
R/metacells.R
R/plotting.R
R/pseudotime.R
README.md
_pkgdown.yml
data/test_seurat.rda
docs/.DS_Store
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docs/articles/basic_tutorial.html
docs/articles/consensus_wgcna.html
docs/articles/customization.html
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inst/CITATION
inst/pkgdown.yml
man/AssignTFRegulons.Rd
man/AvgModuleExpr.Rd
man/BinPseudotime.Rd
man/CheckSeurat5.Rd
man/CheckWGCNAName.Rd
man/ComputeModuleEigengene.Rd
man/ConstructMetacells.Rd
man/ConstructMetaspots.Rd
man/ConstructNetwork.Rd
man/ConstructPseudobulk.Rd
man/ConstructTFNetwork.Rd
man/DimPlotMetacells.Rd
man/DoHubGeneHeatmap.Rd
man/EnrichrBarPlot.Rd
man/EnrichrDotPlot.Rd
man/FindAllDMEs.Rd
man/FindDMEs.Rd
man/FindDifferentialRegulons.Rd
man/FindMajorIsoforms.Rd
man/GetActiveWGCNA.Rd
man/GetActiveWGCNAName.Rd
man/GetAvgModuleExpr.Rd
man/GetDatExpr.Rd
man/GetDegrees.Rd
man/GetEnrichrRegulonTable.Rd
man/GetEnrichrTable.Rd
man/GetHubGenes.Rd
man/GetMELoadings.Rd
man/GetMEs.Rd
man/GetMetacellObject.Rd
man/GetMetacellParams.Rd
man/GetModulePreservation.Rd
man/GetModuleScores.Rd
man/GetModuleTraitCorrelation.Rd
man/GetModuleUMAP.Rd
man/GetModules.Rd
man/GetMotifMatrix.Rd
man/GetMotifOverlap.Rd
man/GetMotifScores.Rd
man/GetMotifTargets.Rd
man/GetMotifs.Rd
man/GetMultiExpr.Rd
man/GetNetworkData.Rd
man/GetPFMList.Rd
man/GetPowerTable.Rd
man/GetRegulonScores.Rd
man/GetTFEval.Rd
man/GetTFNetwork.Rd
man/GetTFRegulons.Rd
man/GetTFTargetGenes.Rd
man/GetTOM.Rd
man/GetWGCNAGenes.Rd
man/GetWGCNAParams.Rd
man/HubGeneNetworkPlot.Rd
man/MetacellsByGroups.Rd
man/MetaspotsByGroups.Rd
man/ModuleConnectivity.Rd
man/ModuleCorrNetwork.Rd
man/ModuleCorrelogram.Rd
man/ModuleEigengenes.Rd
man/ModuleExprScore.Rd
man/ModuleFeaturePlot.Rd
man/ModuleNetworkPlot.Rd
man/ModulePreservation.Rd
man/ModulePreservationNetRep.Rd
man/ModuleRadarPlot.Rd
man/ModuleRegulatoryHeatmap.Rd
man/ModuleRegulatoryNetwork.Rd
man/ModuleRegulatoryNetworkPlot.Rd
man/ModuleTopologyBarplot.Rd
man/ModuleTopologyHeatmap.Rd
man/ModuleTraitCorrelation.Rd
man/ModuleUMAPPlot.Rd
man/MotifOverlapBarPlot.Rd
man/MotifScan.Rd
man/NormalizeMetacells.Rd
man/OverlapBarPlot.Rd
man/OverlapDotPlot.Rd
man/OverlapModulesDEGs.Rd
man/OverlapModulesMotifs.Rd
man/PlotDMEsLollipop.Rd
man/PlotDMEsVolcano.Rd
man/PlotDendrogram.Rd
man/PlotDifferentialRegulons.Rd
man/PlotKMEs.Rd
man/PlotLollipop.Rd
man/PlotModulePreservation.Rd
man/PlotModulePreservationLollipop.Rd
man/PlotModuleTraitCorrelation.Rd
man/PlotModuleTrajectory.Rd
man/PlotSoftPowers.Rd
man/ProjectModules.Rd
man/ReassignModules.Rd
man/RegulonBarPlot.Rd
man/RegulonScores.Rd
man/ResetModuleColors.Rd
man/ResetModuleNames.Rd
man/RunEnrichr.Rd
man/RunEnrichrRegulons.Rd
man/RunHarmonyMetacells.Rd
man/RunModuleUMAP.Rd
man/RunPCAMetacells.Rd
man/RunUMAPMetacells.Rd
man/ScaleMetacells.Rd
man/SelectNetworkGenes.Rd
man/SetActiveWGCNA.Rd
man/SetAvgModuleExpr.Rd
man/SetDatExpr.Rd
man/SetDegrees.Rd
man/SetEnrichrRegulonTable.Rd
man/SetEnrichrTable.Rd
man/SetMELoadings.Rd
man/SetMEs.Rd
man/SetMetacellObject.Rd
man/SetMetacellParams.Rd
man/SetModulePreservation.Rd
man/SetModuleScores.Rd
man/SetModuleTraitCorrelation.Rd
man/SetModuleUMAP.Rd
man/SetModules.Rd
man/SetMotifMatrix.Rd
man/SetMotifOverlap.Rd
man/SetMotifScores.Rd
man/SetMotifTargets.Rd
man/SetMotifs.Rd
man/SetMultiExpr.Rd
man/SetNetworkData.Rd
man/SetPFMList.Rd
man/SetPowerTable.Rd
man/SetRegulonScores.Rd
man/SetTFEval.Rd
man/SetTFNetwork.Rd
man/SetTFRegulons.Rd
man/SetWGCNAGenes.Rd
man/SetWGCNAParams.Rd
man/SetupForWGCNA.Rd
man/TFNetworkPlot.Rd
man/TestSoftPowers.Rd
man/TestSoftPowersConsensus.Rd
man/TransferModuleGenome.Rd
man/check_inputs.Rd
man/corSparse.Rd
man/figures/logo.png
man/logo_v4.png
man/scale01.Rd
man/shuffle_points.Rd
man/to_pseudobulk.Rd
man/umap_theme.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
reference/figures/logo.png
tests/testthat.R
tests/testthat/test-ConstructNetwork.R
tests/testthat/test-Metacells.R
tests/testthat/test-ModuleEigengenes.R
tests/testthat/test-SetDatExpr.R
tests/testthat/test-SetupForWGCNA.R
tests/testthat/test-SoftPowers.R
vignettes/ST_basics.Rmd
vignettes/basic_tutorial.Rmd
vignettes/consensus_wgcna.Rmd
vignettes/customization.Rmd
vignettes/differential_MEs.Rmd
vignettes/enrichment_analysis.Rmd
vignettes/hdWGCNA.Rmd
vignettes/isoform_pbmcs.Rmd
vignettes/module_preservation.Rmd
vignettes/module_trait_correlation.Rmd
vignettes/motif_analysis.Rmd
vignettes/network_visualizations.Rmd
vignettes/other_metacells.Rmd
vignettes/projecting_modules.Rmd
vignettes/projecting_modules_cross.Rmd
vignettes/pseudobulk.Rmd
vignettes/pseudotime.Rmd
vignettes/sctransform.Rmd
vignettes/tf_network.Rmd
