Clustering and Resolution Enhancement of Spatial Transcriptomes


[Up] [Top]

Documentation for package ‘BayesSpace’ version 1.17.0

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