Changes

• Added group.by parameter to FindAllMarkers, allowing users to regroup their data using a non-default identity class prior to performing differential expression (#9550)
• Added image.type parameter to Read10X_Image enabling VisiumV1 instances to be populated instead of instances of the default VisiumV2 class (#9556)
• Fixed IntegrateLayers to respect the dims.to.integrate parameter
• Added stroke.size parameter to DimPlot (#8180)
• Updated RunLeiden to use the leidenbase package instead of leiden; deprecated the method parameter for RunLeiden and FindClusters; updated RunLeiden to reset random.seed to 1 if the value is 0 or less (#6792)
• Updated RunPCA to use the BPCells-provided SVD solver on BPCells matrices; updated JackStraw to support BPCells matrices (#8271)
• Fixed RunPCA to avoid converting BPCells matrices into dense matrices - significantly reduces the function's memory usage when running on BPCells matrices (#8966)
• Updated RunSLSI to support BPCells matrices
• Fixed DietSeurat so that the layers parameter is respected (#8197)
• Updated RunUMAP to support umap-learn version >= 0.5.0 (#9559)
• Updated LoadXenium and ReadXenium to accommodate the output from XOA v3.0; updated LoadXenium to provide more fine-grained control over the datatypes parsed in, including nucleus segmentation masks, segmentation methods, and other experimental metadata; updated ReadXenium to load cell_feature_matrix.h5 when present in favor of the MEX format files; updated ReadXenium to load .parquet files using arrow instead of .csv.gz files to support XOA 3.0 (#8604)
• Fixed LoadXenium to accommodate datasets without "Blank Codeword" or "Unassigned Codeword" matrices(#9135)
• Fixed ReadXenium to properly parse multiple molecular outputs at once (#8265)
• Added features parameter to LeverageScore and SketchData
• Updated SketchData's ncells parameter to accept integer vector