# Spatial transcriptomic clustering

## Documentation for package ‘Banksy’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

clusterBanksy | Perform clustering in BANKSY's neighborhood-augmented feature space.
clusterNames | Get names of clustering runs.
compareClusters | Compare cluster outputs based on various clustering comparison measures.
computeBanksy | Compute the component neighborhood matrices for the BANKSY matrix.
connectClusters | Relabel cluster labels across parameter runs to maximise their similarity.
getBanksyMatrix | Builds the BANKSY matrix from neighborhood matrices.
hippocampus | Mouse Hippocampus VeraFISH data
rings | An unrealistic simulation of spatially-resolved omics data.
runBanksyPCA | Run PCA on a BANKSY matrix.
runBanksyUMAP | Run UMAP on a BANKSY embedding.
simulateDataset | Simulate an unrealistic spatial omics dataset.
smoothLabels | k-Nearest neighbor cluster label smoothing.