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Version 3.1.0

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@mojaveazure mojaveazure released this 20 Aug 21:56
· 5502 commits to master since this release
v3.1.0
c9f2660
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Changes:

  • Bug fixes in LogSeuratCommand, Read10X, UpdateSeuratObject, FeaturePlot, WhichCells, and HoverLocator
  • Prevent dimnames for counts/data/scale.data matrices from being arrays
  • Updates ReadH5AD to distinguish FVF methods
  • Sink all output from stdout to stderr
  • Fix to scale.data cell ordering after subsetting
  • Enable Assay specification in BuildClusterTree
  • Ensure features names don't contain pipes (|)
  • Deprecation of RunLSI and RunALRA
  • Fix legend bug when sorting in ExIPlot

Additions:

  • New PrepSCTIntegration function to facilitate integration after SCTransform
  • Reference-based integration with the reference parameter in FindIntegrationAnchors
  • Reciprocal PCA as a reduction option in FindIntegrationAnchors
  • New CollapseEmbeddingOutliers function
  • Enable FindTransferAnchors after SCTransform
  • Added back ColorDimSplit functionality
  • Include a code of conduct
  • Added uwot support as new default UMAP method
  • Added CheckDots to catch unused parameters and suggest updated names
  • Reductions and Assays assays functions to list stored DimReducs and Assays
Assets 2
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