Man pages for spatialGE
Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression
| compare_SThet | compare_SThet: Compares spatial autocorrelation statistics... |
| dim-STlist-method | dim: Prints the dimensions of count arrays within an STList... |
| distribution_plots | per_unit_counts: Generates distribution plots of spot/cell... |
| 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"... |
| show-STlist-method | show: Prints overview of STList oject. |
| spatial_metadata | spatial_metadata: Prints the names of the available spot/cell... |
| STclust | STclust: Detect clusters of spots/cells |
| STdiff | STdiff: Differential gene expression analysis for spatial... |
| 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... |
| STlist | STlist: Creation of STlist objects for spatial... |
| STlist-class | Definition of an STlist object class. |
| STplot | STplot: Plots of gene expression, cluster memberships, and... |
| STplot_interpolation | STplot_interpolation: Visualize gene expression surfaces |
| summarize_STlist | summarize_STlist: Generates a data frame with summary... |
| summary-STlist-method | summary: Prints overview of STList oject. |
| tissue_names | tissue_names: Prints the names of the tissue samples in the... |
| transform_data | transform_data: Transformation of spatial transcriptomics... |
