satijalab/seurat v5.0.0

on GitHub

Added

• Add BridgeCellsRepresentation to construct a dictionary representation for each unimodal dataset.
• Add BuildNicheAssay to construct a new assay where each feature is a cell label. The values represent the sum of a particular cell label neighboring a given cell.
• Add CalcDispersion to calculate the dispersion of features.
• Add CCAIntegration to perform Seurat-CCA Integration.
• Add CountSketch to generate a CountSketch random matrix.
• Add CreateCategoryMatrix to create a one-hot matrix for a given label.
• Add DISP to find variable features based on dispersion.
• Add FastRPCAIntegration as a convenience wrapper function around the following three functions that are often run together when performing integration.
• Add FetchResiduals_reference as a temporary function to get residuals from the reference.
• Add FetchResiduals to call sctransform::get_residuals.
• Add FetchResidualSCTModel to calculate Pearson residuals of features not in the scale.data.
• Add FindBridgeAnchor to find bridge anchors between two unimodal datasets.
• Add FindBridgeIntegrationAnchors to find a set of anchors for integration between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.
• Add FindBridgeTransferAnchors to find a set of anchors for label transfer between unimodal query and the other unimodal reference using a pre-computed BridgeReferenceSet.
• Add GaussianSketch to perform Gaussian sketching.
• Add HarmonyIntegration to perform Harmony integration.
• Add IntegrateLayers to integrate layers in an assay object.
• Add JointPCAIntegration to perform Seurat-Joint PCA Integration.
• Add LeverageScore to compute the leverage scores for a given object.
• Add LoadCurioSeeker to load Curio Seeker data.
• Add MVP to find variable features based on mean.var.plot.
• Add NNtoGraph to convert the Neighbor class to an asymmetrical Graph class.
• Add PrepareBridgeReference to preprocess the multi-omic bridge and unimodal reference datasets into an extended reference.
• Add ProjectCellEmbeddings to project query data onto the reference dimensional reduction.
• Add ProjectData to project high-dimensional single-cell RNA expression data from a full dataset onto the lower-dimensional embedding of the sketch of the dataset.
• Add ProjectDimReduc to project query data to reference dimensional reduction.
• Add ProjectIntegration to integrate embeddings from the integrated sketched.assay.
• Add PseudobulkExpression to normalize the count data present in a given assay.
• Add Read10X_probe_metadata to read the probe metadata from a 10x Genomics probe barcode matrix file in HDF5 format.
• Add RPCAIntegration to perform Seurat-RPCA Integration.
• Add RunGraphLaplacian to run a graph Laplacian dimensionality reduction.
• Add SelectIntegrationFeatures5 to select integration features for v5 assays.
• Add SelectSCTIntegrationFeatures to select SCT integration features.
• Add SketchData to use sketching methods to downsample high-dimensional single-cell RNA expression data for help with scalability for large datasets.
• Add TransferSketchLabels to transfer cell type labels from a sketched dataset to a full dataset based on the similarities in the lower-dimensional space.
• Add UnSketchEmbeddings to transfer embeddings from sketched cells to the full data.
• Add VST to apply a variance stabilizing transformation for selection of variable features.

Changes

• Change FindTransferAnchors so that anchor filtering is not performed by default
• Change merge so that layers will be added to a single Seurat object instead of combining raw count matrices
• Deprecate slot parameter in favor of layers in accessor and set methods

Full Changelog: v4.4.0...v5.0.0