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NEWS.md

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Version 0.99.8

  • Add feature scaling options for PCA and UMAP

Version 0.99.7

  • SCE/SPE-compatible

Version 0.1.6

  • Fix compatibility with SeuratWrappers

Version 0.1.5

  • Implemented SmoothLabels for k-nearest neighbors cluster label smoothing
  • Parallel clustering for Leiden graph-based clustering
  • Version depedency on leidenAlg (>= 1.1.0) for compatibility with igraph (>= 1.5.0)
  • Seed setting for clustering
  • Neighborhood sampling for computing neighborhood feature matrices. See arguments sample_size, sample_renorm and seed in function ComputeBanksy

Version 0.1.4

  • Implemented Azimuthal Gabor filters in ComputeBanksy, with the number of harmonics determined by the M argument. To obtain similar results as version 0.1.3, use M=0
  • RunPCA and RunUMAP renamed to RunBanksyPCA and RunBanksyUMAP respectively to avoid namespace collisions with other packages
  • Changed some function argument names (e.g. spatialMode to spatial_mode)

Version 0.1.3

  • Interoperability with SingleCellExperiment with asBanksyObject
  • Passing Bioc and R CMD checks

Version 0.1.2

  • BanksyObject: dimensionality reduction slot name changed to reduction
  • RunPCA and RunUMAP
  • Plotting is generalised (plotReduction instead of plotUMAP / plotPCA)
  • ConnectClusters improved and returns BanksyObject
  • ARI computation and plotting

Version 0.0.9

  • Legacy version