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@mojaveazure mojaveazure released this 01 Feb 01:46
· 2536 commits to master since this release
v4.0.0
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Learn about vigilant mode.

Changes

  • Removed old, deprecated code
  • Utilize SeuratObject as base of object code
  • Default neighbor finding algorithm changed from "rann" to "annoy"
  • Default ncells parameter in SCTransform() changed to 5000
  • Default fold change in FindMarkers() changed from ln to log2
  • Implementation improvements to AverageExpression()
  • AnchorSet class re-implemented as a virtual class from which IntegrationAnchorSet and TransferAnchorSet now inherit.
  • Point size in VlnPlot() now set automatically if not specified
  • Return the sample.tree properly when integrating with a single reference dataset
  • Replace as.character.quosure usage with as_label due to deprecation
  • Minor changes to the exact calculation of the anchor weight matrix
  • Default rasterization limit in DimPlot() and FeaturePlot() changed from 50,000 to 100,000
  • SCTransform() now returns a formalized Assay subclass SCTAssay()
  • When using normalization.method='SCT' in FindTransferAnchors(), normalize query using reference SCT model when possible.

Additions

  • Expose FoldChange() component in FindMarkers()
  • Add IntegrateEmbeddings() to correct embeddings of DimReducs
  • Add ProjectUMAP() to project query cells into a reference UMAP space
  • Add MapQuery() as a wrapper around IntegrateData(), IntegrateEmbeddings(), and ProjectUMAP()
  • Add MappingScore to compute a per-cell mapping score used in Azimuth
  • Add AggregateExpression() for summation based pseudobulk calculations
  • Add mixscape functionality via CalcPerturbSig(), PrepLDA(), RunLDA(), DEenrichRPlot(), MixscapeHeatmap(), MixscapeLDA(), PlotPerturbScore(), RunMixscape()
  • Add FindSubCluster() to further cluster existing clusters
  • Add supervised PCA functionality via RunSPCA()
  • Add functionality to enable weighted nearest neighbor analyses via FindMultiModalNeighbors()
  • Add neighbor visualization plot via NNPlot().
  • Add PredictAssay() to impute expression or embeddings from nearest neighbors
  • Add AnnotateAnchors() to aid in AnchorSet interpretation as well as subset.AnchorSet()
  • Add flexibility of choice for cell column in Read10X()
  • Add rasterization option to FeatureScatter() and VariableFeaturePlot()
Assets 2