Package index • spatialGE

All functions
`STclust()`	STclust: Detect clusters of spots/cells
`STdiff()`	STdiff: Differential gene expression analysis for spatial transcriptomics data
`STdiff_volcano()`	STdiff_volcano: Generates volcano plots from STdiff results
`STenrich()`	STenrich
`STgradient()`	STgradient: Tests of gene expression spatial gradients
`SThet()`	SThet: Computes global spatial autocorrelation statistics on gene expression
`STlist-class`	Definition of an STlist object class.
`STlist()`	STlist: Creation of STlist objects for spatial transcriptomics analysis
`STlist_to_disk()`	STlist_to_disk: Move an STlist's count matrices to on-disk parquet
`STlist_to_memory()`	STlist_to_memory: Bring an on-disk STlist back into memory
`STniche()`	STniche (mclust version): Detect functional spatial domains with model-based clustering
`STplot()`	STplot: Plots of gene expression, cluster memberships, and metadata in spatial context
`STplot_interpolation()`	STplot_interpolation: Visualize gene expression surfaces
`as_Seurat()`	as_Seurat: Convert an STlist to a Seurat object
`compare_SThet()`	compare_SThet: Compares spatial autocorrelation statistics across samples
`dim(<STlist>)`	dim: Prints the dimensions of count arrays within an STList object.
`distribution_plots()`	per_unit_counts: Generates distribution plots of spot/cell meta data or gene expression
`filter_data()`	filter_data: Filters cells/spots, genes, or samples
`gene_interpolation()`	gene_interpolation: Spatial interpolation of gene expression
`get_gene_meta()`	get_gene_meta: Extract gene-level metadata and statistics
`is_backed()`	is_backed: Is an STlist's expression data stored on disk?
`load_images()`	load_images: Place tissue images within STlist
`plot_counts()`	plot_counts: Generates plots for the distribution of counts
`plot_image()`	plot_image: Generate a ggplot object of the tissue image
`plot_stniche()`	Plot STniche results
`pseudobulk_dim_plot()`	pseudobulk_dim_plot: Plot PCA of pseudobulk samples
`pseudobulk_heatmap()`	pseudobulk_heatmap: Heatmap of pseudobulk samples
`pseudobulk_samples()`	pseudobulk_samples: Aggregates counts into "pseudo bulk" samples
`show(<STlist>)`	show: Prints overview of STList oject.
`spatial_metadata()`	spatial_metadata: Prints the names of the available spot/cell annotations
`summarize_STlist()`	summarize_STlist: Generates a data frame with summary statistics
`summary(<STlist>)`	summary: Prints overview of STList oject.
`tissue_names()`	tissue_names: Prints the names of the tissue samples in the STlist
`transform_data()`	transform_data: Transformation of spatial transcriptomics data
`validate_store()`	validate_store: Check an on-disk STlist against its manifests

Reference

All functions