Reference

Spatial analysis

spatialPreprocess()

Preprocess a spatial dataset for BayesSpace

spatialCluster()

Spatial clustering

spatialEnhance()

Enhance spot resolution

enhanceFeatures()

Predict feature vectors from enhanced PCs.

Visualization

clusterPlot()

Plot spatial cluster assignments.

featurePlot()

Plot spatial gene expression.

Model tuning and inspection

qPlot() qTune()

Tuning the choice of q (number of clusters) before running spatialCluster

mcmcChain() removeChain()

Read MCMC chain associated with a BayesSpace clustering or enhancement

Loading datasets

getRDS()

Download a processed sample from our S3 bucket

readVisium()

Load a Visium spatial dataset as a SingleCellExperiment.

exampleSCE()

Create minimal SingleCellExperiment for documentation examples.