Banksy - v1.5.8

This release implements scalability improvements. - Implements margin for chunking (855c3102938ad95726621ae04042ced2d079c435) - Implements sparse matrix support (098ad3f371861c10c337c7e409b79bfa7327dfe0)

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Published by jleechung 7 months ago

Banksy - v.1.5.3

This release implements minor fixes and scalability improvements. - Fix to use the prop_thres argument in smoothBanksy (9fd772b5482b2bc2eb01201de819b83825a5067a) - Fix to use the center argument computeBanksy (fbb4891010f8555f64c4eb7ece14f633521699a7) - Implements chunking in the feature dimension (fbb4891010f8555f64c4eb7ece14f633521699a7) - Implements optional parallelism for chunking (fbb4891010f8555f64c4eb7ece14f633521699a7)

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Published by jleechung 9 months ago

Banksy - v0.1.6

• Fixed compatibility with SeuratWrappers and bioc versions

- R
Published by jleechung almost 2 years ago

Banksy - v0.1.5

• Cluster label smoothing
• Parallelism for clustering using foreach
• Filtering out samples with NAs in their features on initialisation
• Seed setting for clustering
• Version dependency on leidenAlg (>1.1.0) for compatibility with igraph
• Neighborhood-sampling (see arguments sample_size and sample_renorm for function ComputeBanksy)
• Replacing M with compute_agf and use_agf as arguments for specifying which harmonics to compute

- R
Published by jleechung over 2 years ago

Banksy - v0.1.4

This release implements azimuthal Gabor filters as additional features of a cell's neighborhood.

• Azimuthal Gabor filters implemented in ComputeBanksy, with the number of harmonics determined by the M argument. To obtain similar results as version 0.1.3, use M=0
• Default size factor for NormalizeBanksy is set to the median total count
• RunPCA and RunUMAP renamed to RunBanksyPCA and RunBanksyUMAP respectively to avoid namespace collisions with other packages
• The following argument names have been modified for style:
  • NormalizeBanksy: normFactor to norm_factor
  • NormalizeBanksy: logNorm to log_norm
  • ComputeBanksy: spatialMode to spatial_mode
  • ComputeBanksy: kspatial to k_spatial

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Published by jleechung over 2 years ago

Banksy - v.0.1.3.33

Implements minor fixes and updated documentation from release v.0.1.3.

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Published by jleechung over 2 years ago

Banksy - v.0.1.3

First public release.

Changes from v0.0.9:

• Passing Bioc and R CMD checks
• Implemented: asBanksyObject for interop. with SingleCellExperiment
• Implemented: RunPCA and RunUMAP
• Implemented: plotReduction for generalised plotting
• Implemented: plotARI and getARI for ARI computation and plotting
• Changed: ConnectClusters returns BanksyObject
• Changed: BanksyObject slot dim.reduction to reduction

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Published by jleechung almost 4 years ago

Banksy - v0.0.9

Legacy version of BANKSY.

Main differences between v0.0.9 and v0.1.x:

• BanksyObject: dimensionality reduction slot name dim.reduction (changed to reduction in v0.1.x)
• BanksyObject: no clust.names method
• Dimensionality reduction steps (PCA / UMAP) included in ClusterBanksy now removed as separate functions in v0.1.x
• Plotting is generalised in v0.1.x (plotReduction instead of plotUMAP / plotPCA)
• ConnectClusters implementation improved in v0.1.x and returns only BanksyObject in v0.1.x (instead of list in v.0.0.9)
• ARI computation and plotting is included in v0.1.x (getARI / plotARI)
• Data moved from inst/extdata (v0.0.9) to /data (v.0.1.x)

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Published by jleechung about 4 years ago