# Clustering and Resolution Enhancement of Spatial Transcriptomes

## Documentation for package ‘BayesSpace’ version 1.21.2

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

## Help Pages

adjustClusterLabels | Enhance spot resolution
clusterPlot | Plot spatial cluster assignments.
coreTune | Enhance spot resolution
counts2h5 | Load a Visium spatial dataset as a SingleCellExperiment.
enhanceFeatures | Predict feature vectors from enhanced PCs.
exampleSCE | Create minimal 'SingleCellExperiment' for documentation examples.
featurePlot | Plot spatial gene expression.
getRDS | Download a processed sample from our S3 bucket
mcmcChain | Read MCMC chain associated with a BayesSpace clustering or enhancement
paraLapply | Parallelization
parallelize | Parallelization
qPlot | Tuning the choice of q (number of clusters) before running spatialCluster
qTune | Tuning the choice of q (number of clusters) before running spatialCluster
read10Xh5 | Load a Visium spatial dataset as a SingleCellExperiment.
readVisium | Load a Visium spatial dataset as a SingleCellExperiment.
removeChain | Read MCMC chain associated with a BayesSpace clustering or enhancement
spatialCluster | Spatial clustering
spatialEnhance | Enhance spot resolution
spatialPreprocess | Preprocess a spatial dataset for BayesSpace