Changes in version 0.5.00 (2026-01-24) Added - New vignettes: Introduction, Quick Start Guide, Algorithm and Mathematical Framework - Integrated UCell scoring functionality (removed external UCell dependency) Changes - Complete package review and optimization - Fixed critical bug in ModuleTraitCorrelation for factor variable handling - Fixed logical error in trait length checking - Improved Seurat v4/v5 compatibility across all functions - Optimized RunEnrichr and ConstructTFNetwork performance - Updated author information and package URLs - Cleaned up debug statements and improved code documentation Changes in version 0.4.09 (2026-01-06) Added - None Changes - Improved error handling in the function ModuleTraitCorrelation - Updated the installation instructions in README.md to fix conda environment creation command. - Bugfix in ProjectModules when using a user-defined modules table rather than a reference seurat object. - Bugfix in MetacellsByGroups when using Seurat v5. Changes in version 0.4.08 (2025-10-23) Added - None Changes - Improved error handling in the function EnrichrDotPlot. Changes in version 0.4.07 (2025-09-04) Added - None Changes - Update to ReassignModules to add the option of automatically re-assigning selected genes to the module with the highest kME. Helpful in particular cases where some gene(s) of interest were assigned to the grey module. Changes in version 0.4.06 (2025-06-02) Added - None Changes - Fixed issue with ModuleRadarPlot when group.by is a factor. - Fixed an internal issue with ModulePreservationNetRep. - Updated some typos in the Visium HD tutorial. Changes in version 0.4.05 (2025-03-10) Added - None Changes - Fixed compatibility issue causing an error in ModuleEigengenes when using SCTransform datasets in Seurat v5. Changes in version 0.4.04 (2025-02-21) Added - None Changes - Updated MotifScan to handle cases where one gene name corresponds to multiple motifs. - Updated ConstructTFNetwork for compatible with multiple versions of xgboost. Changes in version 0.4.03 (2025-01-27) Added - New tutorial titled "Integrating co-expression and protein-protein interaction networks". Changes - None. Changes in version 0.4.02 (2025-01-23) Added - RunEnrichrRegulons. This should have been included previously but there was a problem with the export. Changes - Bugfix in PlotModuleTrajectory Changes in version 0.4.01 (2025-01-10) Added - New section in the enrichment tutorial for GSEA analysis. Changes - New options in EnrichrDotPlot and EnrichrBarPlot. - Updated EnrichrDotPlot. Changes in version 0.4.00 (2024-10-09) Added - Transcription Factor Regulatory Network Analysis functionality. Changes in version 0.3.03 (2024-06-07) Added - ModuleRadarPlot function to visualize expression levels of each module. Changes - Bugfix in PlotModuleTraitCorrelation - Update to basics to tutorial to include ModuleRadarPlot Changes in version 0.3.02 (2024-05-28) Added New functionality and methods for module preservation analysis using the NetRep method from Ritchie et al 2016. - ModuleTopologyHeatmap function. - ModuleTopologyBarplot function. - ModulePreservationNetrep function. - PlotModulePreservationLollipop function. Changes - Update to module preservation tutorial to demonstrate how to perform module preservation analysis using NetRep. Changes in version 0.3.01 (2024-03-07) Added - None Changes - Bugfix in ModulePreservation - Update to module preservation tutorial and project modules tutorial. Changes in version 0.3.00 (2024-02-27) Added - First version with support for Seurat v5. - Updated the network visualization tutorial with a tutorial for making custom networks. Changes - Changed FindDMEs and FindAllDMEs to perform differential testing with module expression scores. Changes in version 0.2.27 (2024-01-29) Added - New option to MetacellsByGroups to specify dims. Changes - Fixed HubGeneNetworkPlot to allow selecting specific modules. - GetHubGenes now returns genes in order from highest to lowest kME in each module. Changes in version 0.2.26 (2023-12-05) Added - None Changes - New options for changing colors in EnrichrBarPlot. - ConstructNetwork naming of temporary files updated. Changes in version 0.2.25 (2023-11-28) Added - None Changes - Requires Seurat version 4. Will update to support v5 in the future. Changes in version 0.2.24 (2023-09-28) Added - None Changes - Update call to Harmony in ModuleEigengenes function Changes in version 0.2.23 (2023-09-10) Added - None Changes - Fixed bug in SetDatExpr Changes in version 0.2.22 (2023-09-08) Added - New tutorial for hdWGCNA with pseudobulk data, including some new functions like ConstructPseudobulk. Changes - Updated SetDatExpr and SetMultiExpr to use a pseudobulk expression matrix. Changes in version 0.2.21 (2023-08-31) Added - 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. Changes - None. Changes in version 0.2.20 (2023-08-17) Added - None. Changes - Dependency for tester pacakge. Changes in version 0.2.19 (2023-06-13) Added - None. Changes - Updated README to include publication, and fixed several igraph function calls. Changes in version 0.2.18 (2023-04-14) Added - None. Changes - We noticed on rare occasion that EnrichR would give duplicated results for different modules, so we added a new option in RunEnrichr to wait in between sending requests to the EnrichR server (default is 5 seconds). Changes in version 0.2.17 (2023-03-27) Added - None. Changes - New error checks in SetupForWGCNA and SelectNetworkGenes Changes in version 0.2.16 (2023-03-20) Added - PlotDMEsLollipop function to visualize differential module eigengenes. Changes - New error checks in MetacellsByGroups Changes in version 0.2.15 (2023-03-02) Added - None Changes - Bugfix to allow ResetModuleNames and ResetModuleColors to work when a grey module is not present. Changes in version 0.2.14 (2023-02-14) Added - None Changes - Fixed a bug in SetDatExpr that would throw an error when group.by=NULL was selected. Changes in version 0.2.13 (2023-02-13) Added - None Changes - Fixed a bug in ReassignModules that cause some modules assignments to be NA for some genes. Changes in version 0.2.12 (2023-02-04) Added - Module eigengene dynamics with pseudotime tutorial - PlotModuleTrajectory function. Changes - None. Changes in version 0.2.11 (2023-01-30) Added - MAS-Seq tutorial (still under construction) Changes - Bugfix in ModuleConnectivity and ReassignModules. Changes in version 0.2.03 (2022-12-15) Added - None Changes - Fixed a bug in ResetModuleNames. Added - None Changes - New error checking in MetaspotsByGroups - MetacellsByGroups now keeps track of which cells were merged. Changes in version 0.2.02 (2022-11-01) Added - None Changes - New warning in SetupForWGCNA if the user selects a very small number of genes. - MetaspotsByGroups uses sparse matrix format internally. Changes in version 0.2.01 (2022-10-06) Added - None Changes - Bugfix in MetaspotsByGroups. Changes in version 0.2.1 (2023-01-24) Added - 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. Changes in version 0.2.00 (2022-09-23) Added - MetaspotsByGroups to aggregate neighboring ST spots prior to network analysis. - Tutorial for applying hdWGCNA to spatial transcriptomics datasets. Changes - None Changes in version 0.1.2.0001 (2022-09-19) Added - None Changes - networkType option in TestSoftPowers. Changes in version 0.1.2.0000 (2022-09-08) Added - Differential Module Eigengene (DME) tutorial - FindDMEs function - FindAllDMEs function - PlotDMEsVolcano function Changes - None Changes in version 0.1.1.9015 (2022-09-06) Added - 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. Changes in version 0.1.1.9014 (2022-08-26) Added - None Changes - Bugfix in ModuleConnectivity that caused kMEs to be out of order. Changes in version 0.1.1.9013 (2022-08-25) Added - Tutorial for using SCTransform normalized data. Changes - None Changes in version 0.1.1.9012 (2022-08-24) Added - None Changes - Now includes options for other types of correlations in ModuleConnectivity. Changes in version 0.1.1.9011 (2022-08-17) Added - 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. Changes in version 0.1.1.9010 (2022-07-30) Added - None Changes - By default, ModuleEigengenes does not compute MEs for the grey module. User can change behavior with the exclude_grey flag. Changes in version 0.1.1.9009 (2022-07-23) Added - None Changes - Bugfix in ProjectModules. - Bugfix in MetacellsByGroups Changes in version 0.1.1.9008 (2022-07-21) Added - 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. Changes in version 0.1.1.9007 (2022-07-20) Added - 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. Changes in version 0.1.1.9006 (2022-07-14) Added - None Changes - ConstructNetwork now checks if the TOM file already exists, and whether the user wants to overwrite the existing TOM. Changes in version 0.1.1.9005 (2022-06-17) Added - 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). Changes in version 0.1.1.9004 Added - None Changes - Bug fix so ModuleTraitCorrelation can be run with a single trait. Changes in version 0.1.1.9003 Added - 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. Changes in version 0.1.1.9002 Added - ModuleEigengenes checks to make sure the data has been scaled. Changes - None Changes in version 0.1.1.9001 (2022-05-09) Added - Wrote docstring for PlotKMEs so it would actually be included in the package. Changes - None Changes in version 0.1.1.9000 (2022-05-05) Added - PlotKMEs function to visualize the genes in a module ranked by kME. Changes - 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. Changes in version 0.0.0.9000 (2021-07-15) - The original (and now unsupported) version of scWGCNA included released in Nature Genetics paper.