NEWS.md

In prabhakarlab/Banksy: Spatial transcriptomic clustering

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

prabhakarlab/Banksy documentation built on May 17, 2024, 12:26 a.m.