- Transcription Factor Regulatory Network Analysis functionality.
ModuleRadarPlotfunction to visualize expression levels of each module.
- Bugfix in
PlotModuleTraitCorrelation - Update to basics to tutorial to include
ModuleRadarPlot
New functionality and methods for module preservation analysis using the NetRep method from Ritchie et al 2016.
ModuleTopologyHeatmapfunction.ModuleTopologyBarplotfunction.ModulePreservationNetrepfunction.PlotModulePreservationLollipopfunction.
- Update to module preservation tutorial to demonstrate how to perform module preservation analysis using NetRep.
- None
- Bugfix in
ModulePreservation - Update to module preservation tutorial and project modules tutorial.
- First version with support for Seurat v5.
- Updated the network visualization tutorial with a tutorial for making custom networks.
- Changed
FindDMEsandFindAllDMEsto perform differential testing with module expression scores.
- New option to
MetacellsByGroupsto specifydims.
- Fixed
HubGeneNetworkPlotto allow selecting specific modules. GetHubGenesnow returns genes in order from highest to lowest kME in each module.
- None
- New options for changing colors in
EnrichrBarPlot. ConstructNetworknaming of temporary files updated.
- None
- Requires Seurat version 4. Will update to support v5 in the future.
- None
- Update call to Harmony in ModuleEigengenes function
- None
- Fixed bug in SetDatExpr
- New tutorial for hdWGCNA with pseudobulk data, including some new functions like
ConstructPseudobulk.
- Updated
SetDatExprandSetMultiExprto use a pseudobulk expression matrix.
- Additional checks for wgcna_name in several functions.
- New section to the DME tutorial to show how to run it in a loop for multiple clusters.
- None.
- None.
- Dependency for tester pacakge.
- None.
- Updated README to include publication, and fixed several igraph function calls.
- None.
- We noticed on rare occasion that EnrichR would give duplicated results for different modules, so we added a new option in
RunEnrichrto wait in between sending requests to the EnrichR server (default is 5 seconds).
- None.
- New error checks in
SetupForWGCNAandSelectNetworkGenes
PlotDMEsLollipopfunction to visualize differential module eigengenes.
- New error checks in
MetacellsByGroups
- None
- Bugfix to allow
ResetModuleNamesandResetModuleColorsto work when a grey module is not present.
- None
- Fixed a bug in
SetDatExprthat would throw an error when group.by=NULL was selected.
- None
- Fixed a bug in
ReassignModulesthat cause some modules assignments to be NA for some genes.
- Module eigengene dynamics with pseudotime tutorial
PlotModuleTrajectoryfunction.
- None.
- MAS-Seq tutorial (still under construction)
- Bugfix in
ModuleConnectivityandReassignModules.
ReassignModulesfunction.
- New option in
ModuleConnectivityto usecorSparseto compute the correlation, which greatly reduces runtime and memory usage. - New option in
ModuleConnectivityto automatically reassign features to different modules if kME is negative.
- None
- Fixed a bug in
ResetModuleNames.
- None
- New error checking in
MetaspotsByGroups MetacellsByGroupsnow keeps track of which cells were merged.
- None
- New warning in
SetupForWGCNAif the user selects a very small number of genes. MetaspotsByGroupsuses sparse matrix format internally.
- None
- Bugfix in
MetaspotsByGroups.
MetaspotsByGroupsto aggregate neighboring ST spots prior to network analysis.- Tutorial for applying hdWGCNA to spatial transcriptomics datasets.
- None
- None
- networkType option in
TestSoftPowers.
- Differential Module Eigengene (DME) tutorial
- FindDMEs function
- FindAllDMEs function
- PlotDMEsVolcano function
- None
- None
- New data format check in
MetacellsByGroupsto ensure that the selected slot is present in the selected assay. SetDatExprnow backs up to the full dataset if the metacell dataset isn't found.- Changed some text to clarify some points in the Module Preservation tutorial.
- None
- Bugfix in
ModuleConnectivitythat caused kMEs to be out of order.
- Tutorial for using SCTransform normalized data.
- None
- None
- Now includes options for other types of correlations in
ModuleConnectivity.
- None
- Reverted the
exclude_greyflag back to doing nothing in theModuleEigengenesfunction because it messed up some downstream tasks, will resolve in a future update. ProjectModulesnow excludes modules with too many missing genes in the query dataset, tunable by theoverlap_proportionparameter.
- None
- By default,
ModuleEigengenesdoes not compute MEs for the grey module. User can change behavior with theexclude_greyflag.
- None
- Bugfix in
ProjectModules. - Bugfix in
MetacellsByGroups
- New tutorial for consensus co-expression network analysis.
ModuleNetworkPlotandRunModuleUMAPnow checks ifModuleConnectivityhas been computed in order to throw a more informative error.GetTOMchecks if the TOM file exists in order to throw a more informative error.
- None
- New warning message in
MetacellsByGroupsif there are any groups that are excluded bymin_cells. - Assay in Metacell seurat object is now the same as the assay supplied to
MetacellsByGroups, instead of the default "RNA". ModuleEigengenestakesassayas an argument, clears up some issues withRunHarmony.ModuleEigengenesdoesn't require a "counts" slot to be present in the given assay, but now it throws an error if the normalized data slot is missing.
- None
ConstructNetworknow checks if the TOM file already exists, and whether the user wants to overwrite the existing TOM.
- None
- Added new arguments to
MetacellsByGroupsandConstructMetacellsto exclude very small groups (min_cells), to reach a target number of metacells (target_metacells), and to exclude metacells with too much overlap (max_shared).
- None
- Bug fix so
ModuleTraitCorrelationcan be run with a single trait.
GetHubGenesfunction to extract the top hub genes from the module assignment table.
ConstructMetacellsstores run statistics as a table, and has a new option to exclude metacells that overlap with each other.
ModuleEigengeneschecks to make sure the data has been scaled.
- None
- Wrote docstring for
PlotKMEsso it would actually be included in the package.
- None
PlotKMEsfunction to visualize the genes in a module ranked by kME.
- Changed the name of the package from scWGCNA to hdWGCNA, since we plan to accommodate data types beyond single cell alone.
- Updated tutorial to recommend computing kMEs in a specific cell population.
- The original (and now unsupported) version of scWGCNA included released in Nature Genetics paper.