Clustering and Resolution Enhancement of Spatial Transcriptomes

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Documentation for package ‘BayesSpace’ version 1.17.0

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

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