• MAS-Seq tutorial (still under construction)

### Changes

• Bugfix in ModuleConnectivity and ReassignModules.

• ReassignModules function.

### Changes

• New option in ModuleConnectivity to use corSparse to compute the correlation, which greatly reduces runtime and memory usage.
• New option in ModuleConnectivity to automatically reassign features to different modules if kME is negative.

• None

### Changes

• Fixed a bug in ResetModuleNames.

• None

### Changes

• New error checking in MetaspotsByGroups
• MetacellsByGroups now keeps track of which cells were merged.

• None

### Changes

• New warning in SetupForWGCNA if the user selects a very small number of genes.
• MetaspotsByGroups uses sparse matrix format internally.

• None

### Changes

• Bugfix in MetaspotsByGroups.

• MetaspotsByGroups to aggregate neighboring ST spots prior to network analysis.
• Tutorial for applying hdWGCNA to spatial transcriptomics datasets.

• None

• None

### Changes

• networkType option in TestSoftPowers.

• Differential Module Eigengene (DME) tutorial
• FindDMEs function
• FindAllDMEs function
• PlotDMEsVolcano function

• None

• None

### Changes

• New data format check in MetacellsByGroups to ensure that the selected slot is present in the selected assay.
• SetDatExpr now 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

### Changes

• Bugfix in ModuleConnectivity that caused kMEs to be out of order.

• Tutorial for using SCTransform normalized data.

• None

• None

### Changes

• Now includes options for other types of correlations in ModuleConnectivity.

• None

### Changes

• Reverted the exclude_grey flag back to doing nothing in the ModuleEigengenes function because it messed up some downstream tasks, will resolve in a future update.
• ProjectModules now excludes modules with too many missing genes in the query dataset, tunable by the overlap_proportion parameter.

• None

### Changes

• By default, ModuleEigengenes does not compute MEs for the grey module. User can change behavior with the exclude_grey flag.

• None

### Changes

• Bugfix in ProjectModules.
• Bugfix in MetacellsByGroups

• New tutorial for consensus co-expression network analysis.

### Changes

• ModuleNetworkPlot and RunModuleUMAP now checks if ModuleConnectivity has been computed in order to throw a more informative error.
• GetTOM checks if the TOM file exists in order to throw a more informative error.

• None

### Changes

• New warning message in MetacellsByGroups if there are any groups that are excluded by min_cells.
• Assay in Metacell seurat object is now the same as the assay supplied to MetacellsByGroups, instead of the default “RNA”.
• ModuleEigengenes takes assay as an argument, clears up some issues with RunHarmony.
• ModuleEigengenes doesn’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

### Changes

• ConstructNetwork now checks if the TOM file already exists, and whether the user wants to overwrite the existing TOM.

• None

### Changes

• Added new arguments to MetacellsByGroups and ConstructMetacells to 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

### Changes

• Bug fix so ModuleTraitCorrelation can be run with a single trait.

• GetHubGenes function to extract the top hub genes from the module assignment table.

### Changes

• ConstructMetacells stores run statistics as a table, and has a new option to exclude metacells that overlap with each other.

• ModuleEigengenes checks to make sure the data has been scaled.

### Changes

• None

• Wrote docstring for PlotKMEs so it would actually be included in the package.

### Changes

• None

• PlotKMEs function to visualize the genes in a module ranked by kME.