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                  STlist: Creation of STlist objects for spatial
                        transcriptomics analysis
STlist-class            Definition of an STlist object class.
STplot                  STplot: Plots of gene expression, cluster
                        memberships, and metadata in spatial context
STplot_interpolation    STplot_interpolation: Visualize gene expression
                        surfaces
compare_SThet           compare_SThet: Compares spatial autocorrelation
                        statistics across samples
dim,STlist-method       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
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
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-method      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-method   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
