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@saketkc saketkc released this 05 Nov 01:47
· 350 commits to master since this release
v5.0.0
ca4c48b

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

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