NEWS.md

In smorabit/scWGCNA: hdWGCNA

hdWGCNA 0.3.01 (2024-03-07)

Added

• None

Changes

• Bugfix in ModulePreservation
• Update to module preservation tutorial and project modules tutorial.

hdWGCNA 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.

hdWGCNA 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.

hdWGCNA 0.2.26 (2023-12-05)

Added

• None

Changes

• New options for changing colors in EnrichrBarPlot.
• ConstructNetwork naming of temporary files updated.

hdWGCNA 0.2.25 (2023-11-28)

Added

• None

Changes

• Requires Seurat version 4. Will update to support v5 in the future.

hdWGCNA 0.2.24 (2023-09-28)

Added

• None

Changes

• Update call to Harmony in ModuleEigengenes function

hdWGCNA 0.2.23 (2023-09-10)

Added

• None

Changes

• Fixed bug in SetDatExpr

hdWGCNA 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.

hdWGCNA 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.

hdWGCNA 0.2.20 (2023-08-17)

Added

• None.

Changes

• Dependency for tester pacakge.

hdWGCNA 0.2.19 (2023-06-13)

Added

• None.

Changes

• Updated README to include publication, and fixed several igraph function calls.

hdWGCNA 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).

hdWGCNA 0.2.17 (2023-03-27)

Added

• None.

Changes

• New error checks in SetupForWGCNA and SelectNetworkGenes

hdWGCNA 0.2.16 (2023-03-20)

Added

• PlotDMEsLollipop function to visualize differential module eigengenes.

Changes

• New error checks in MetacellsByGroups

hdWGCNA 0.2.15 (2023-03-02)

Added

• None

Changes

• Bugfix to allow ResetModuleNames and ResetModuleColors to work when a grey module is not present.

hdWGCNA 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.

hdWGCNA 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.

hdWGCNA 0.2.12 (2023-02-04)

Added

• Module eigengene dynamics with pseudotime tutorial
• PlotModuleTrajectory function.

Changes

• None.

hdWGCNA 0.2.11 (2023-01-30)

Added

• MAS-Seq tutorial (still under construction)

Changes

• Bugfix in ModuleConnectivity and ReassignModules.

hdWGCNA 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.

hdWGCNA 0.2.03 (2022-12-15)

Added

• None

Changes

• Fixed a bug in ResetModuleNames.

hdWGCNA 0.2.03 (2022-11-10)

Added

• None

Changes

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

hdWGCNA 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.

hdWGCNA 0.2.01 (2022-10-06)

Added

• None

Changes

• Bugfix in MetaspotsByGroups.

hdWGCNA 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

hdWGCNA 0.1.2.0001 (2022-09-19)

Added

• None

Changes

• networkType option in TestSoftPowers.

hdWGCNA 0.1.2.0000 (2022-09-08)

Added

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

Changes

• None

hdWGCNA 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.

hdWGCNA 0.1.1.9014 (2022-08-26)

Added

• None

Changes

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

hdWGCNA 0.1.1.9013 (2022-08-25)

Added

• Tutorial for using SCTransform normalized data.

Changes

• None

hdWGCNA 0.1.1.9012 (2022-08-24)

Added

• None

Changes

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

hdWGCNA 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.

hdWGCNA 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.

hdWGCNA 0.1.1.9009 (2022-07-23)

Added

• None

Changes

• Bugfix in ProjectModules.
• Bugfix in MetacellsByGroups

hdWGCNA 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.

hdWGCNA 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.

hdWGCNA 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.

hdWGCNA 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).

hdWGCNA 0.1.1.9004 (2022-6-13)

Added

• None

Changes

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

hdWGCNA 0.1.1.9003 (2022-6-11)

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.

hdWGCNA 0.1.1.9002 (2022-5-24)

Added

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

Changes

• None

hdWGCNA 0.1.1.9001 (2022-05-09)

Added

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

Changes

• None

hdWGCNA 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.

scWGCNA 0.0.0.9000 (2021-07-15)

• The original (and now unsupported) version of scWGCNA included released in Nature Genetics paper.

smorabit/scWGCNA documentation built on April 4, 2024, 10:32 a.m.