API for FridleyLab/spatialGE
Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression
| Global functions | |
|---|---|
| STclust | Man page Source code |
| STdiff | Man page Source code |
| STdiff_volcano | Man page Source code |
| STenrich | Man page Source code |
| STenrich_OLD2 | Source code |
| STenrich_old | Source code |
| STgradient | Man page Source code |
| SThet | Man page Source code |
| SThet_invdist_test | Source code |
| STlist | Man page Source code |
| STlist-class | Man page |
| STplot | Man page Source code |
| STplot_interpolation | Man page Source code |
| Seurat_FindVariableFeatures | Source code |
| SparseRowVar2 | Source code |
| SparseRowVarStd | Source code |
| calculate_dist_matrices | Source code |
| calculate_euclidean_distances | Source code Source code |
| calculate_gs_gsva_score | Source code Source code |
| calculate_gs_mean_exp | Source code Source code |
| calculate_sum_distances | Source code Source code |
| calculate_vst | Source code |
| calculate_weighted_dist | Source code |
| cluster_gene_plots | Source code |
| color_parse | Source code |
| compare_SThet | Man page Source code |
| computeSubsampleSums | Source code |
| count_cores | Source code |
| create_listw | Source code |
| create_listw_from_dist | Source code |
| create_listw_from_knn | Source code |
| detect_input | Source code |
| detect_input_rnacounts | Source code |
| detect_input_samples | Source code |
| detect_input_spotcoords | Source code |
| dim,STlist-method | Man page |
| distribution_plots | Man page Source code |
| expandSparse | Source code |
| filter_data | Man page Source code |
| gene_geary_c | Source code |
| gene_geary_c_dist | Source code |
| gene_geary_c_notest | Source code |
| gene_interpolation | Man page Source code |
| gene_moran_i | Source code |
| gene_moran_i_dist | Source code |
| gene_moran_i_notest | Source code |
| gene_plots | Source code |
| get_gene_meta | Man page Source code |
| get_hier_clusters_dtc | Source code |
| get_hier_clusters_ks | Source code |
| import_smi | Source code |
| import_visium | Source code Source code |
| krige_p | Source code |
| load_images | Man page Source code |
| log_transf | Source code |
| makeSparse | Source code |
| non_spatial_de | Source code |
| old_SThet | Source code |
| plot_counts | Man page Source code |
| plot_image | Man page Source code |
| plot_spatial_expression | Source code |
| plot_spatial_geneset | Source code |
| plot_spatial_meta | Source code |
| prepare_pseudobulk_meta | Source code |
| prepare_stdiff_combo | Source code |
| process_lists | Source code |
| process_meta | Source code |
| process_sample_filepaths | Source code |
| process_sample_names | Source code |
| process_sample_names_from_file | Source code |
| pseudobulk_dim_plot | Man page Source code |
| pseudobulk_heatmap | Man page Source code |
| pseudobulk_samples | Man page Source code |
| quilt_p | Source code |
| raise_err | Source code |
| read_cosmx_input | Source code |
| read_list_dfs | Source code |
| read_matrices_fps | Source code |
| read_seurat | Source code |
| read_visium_outs | Source code |
| read_xenium_outs | Source code |
| sct_transf | Source code |
| show,STlist-method | Man page |
| spatial_de | Source code |
| spatial_metadata | Man page Source code |
| spatial_stat_plot_gene | Source code |
| spot_plots | Source code |
| stdiff_mean_test | Source code |
| summarize_STlist | Man page Source code |
| summary,STlist-method | Man page |
| tissue_names | Man page Source code |
| transform_data | Man page Source code |
