Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

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Documentation for package ‘spatialGE’ version 1.2.2

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

Help Pages

compare_SThet	compare_SThet: Compares spatial autocorrelation statistics across samples
dim-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-method	show: Prints overview of STList oject.
spatial_metadata	spatial_metadata: Prints the names of the available spot/cell annotations
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
summarize_STlist	summarize_STlist: Generates a data frame with summary statistics
summary-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