Files in FridleyLab/spatialGE
Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/.DS_Store

R/RcppExports.R R/STList.R R/STclust.R R/STdiff.R R/STdiff_volcano.R R/STenrich.R R/STenrich_OLD.R R/STenrich_OLD2.R R/STgradient.R R/SThet.R R/SThet_invdist_test.R R/STplot.R R/STplot_interpolation.R R/classDefinitions.R R/compare_SThet.R R/detect_input.R R/distribution_plots.R R/filter_data.R R/gene_interpolation.R R/globals.R R/import_smi.R R/import_visium.R R/import_xenium.R R/old_SThet.R R/plot_counts.R R/plot_helpers.R R/plot_image.R R/plot_spatial_expression.R R/plot_spatial_geneset.R R/plot_spatial_meta.R R/pseudobulk_samples.R R/seurat_helpers.R R/summarize_STlist.R R/transform_data.R R/utils.R R/zzz.R README.md

docs/.DS_Store

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/apple-touch-icon-120x120.png

docs/apple-touch-icon-152x152.png

docs/apple-touch-icon-180x180.png

docs/apple-touch-icon-60x60.png

docs/apple-touch-icon-76x76.png

docs/apple-touch-icon.png

docs/articles/.DS_Store

docs/articles/basic_functions_vignette.html

docs/articles/basic_functions_vignette_files/dir_structure.png

docs/articles/basic_functions_vignette_files/figure-html/clinplot_chunk-1.png

docs/articles/basic_functions_vignette_files/figure-html/count_dstr-1.png

docs/articles/basic_functions_vignette_files/figure-html/filter_chunk-1.png

docs/articles/basic_functions_vignette_files/figure-html/genequilt_chunk2-1.png

docs/articles/basic_functions_vignette_files/figure-html/heatmap_chunk-1.png

docs/articles/basic_functions_vignette_files/figure-html/pca_chunk-1.png

docs/articles/basic_functions_vignette_files/figure-html/plot_tissue-1.png

docs/articles/basic_functions_vignette_files/figure-html/plotclustspots_chunk-1.png

docs/articles/basic_functions_vignette_files/figure-html/plotkrige_chunk1-1.png

docs/articles/basic_functions_vignette_files/figure-html/tissue_sim_2-1.png

docs/articles/basic_functions_vignette_files/figure-html/tissue_sim_4-1.png

docs/articles/basic_functions_vignette_files/kePrint-0.0.1/kePrint.js

docs/articles/basic_functions_vignette_files/lightable-0.0.1/lightable.css

docs/articles/basic_functions_vignette_files/metadata_file.png

docs/articles/img/diagram_stenrich.png

docs/articles/img/dir_structure.png

docs/articles/img/metadata_file.png

docs/articles/img/smi_dir_structure.png

docs/articles/img/spatial_gradients.png

docs/articles/index.html

docs/articles/spatial_differential_expression.html

docs/articles/spatial_differential_expression_files/figure-html/compare_pval_p-1.png

docs/articles/spatial_differential_expression_files/figure-html/plotclustspots_chunk-1.png

docs/articles/spatial_differential_expression_files/figure-html/vgm_model_plot-1.png

docs/articles/spatial_differential_expression_files/figure-html/vgm_plot-1.png

docs/articles/spatial_differential_expression_files/figure-html/volc_plots2-1.png

docs/articles/spatial_enrichment_gradients_smi.html

docs/articles/spatial_enrichment_gradients_smi_files/figure-html/count_dstr-1.png

docs/articles/spatial_enrichment_gradients_smi_files/figure-html/notch_plots-1.png

docs/articles/spatial_enrichment_gradients_smi_files/figure-html/plot_domains-1.png

docs/articles/spatial_enrichment_gradients_smi_files/figure-html/stg_plots-1.png

docs/articles/spatial_enrichment_gradients_smi_files/figure-html/unnamed-chunk-1-1.png

docs/articles/troubleshooting.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.1.0/bootstrap.min.css

docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/diagram_stenrich.png

docs/dir_structure.png

docs/docsearch.css

docs/docsearch.js

docs/favicon-16x16.png

docs/favicon-32x32.png

docs/favicon.ico

docs/index.html

docs/link.svg

docs/logo.png

docs/metadata_file.png

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/STclust-1.png

docs/reference/STclust.html

docs/reference/STdiff.html

docs/reference/STdiff_volcano.html

docs/reference/STenrich.html

docs/reference/STgradient.html

docs/reference/SThet.html

docs/reference/SThet_invdist_test.html

docs/reference/STlist-class.html

docs/reference/STlist.html

docs/reference/STplot-1.png

docs/reference/STplot.html

docs/reference/STplot_interpolation-1.png

docs/reference/STplot_interpolation.html

docs/reference/compare_SThet.html

docs/reference/dim-STlist-method.html

docs/reference/distribution_plots.html

docs/reference/filter_data.html

docs/reference/gene_interpolation-1.png

docs/reference/gene_interpolation.html

docs/reference/get_gene_meta.html

docs/reference/index.html

docs/reference/load_images.html

docs/reference/old_SThet.html

docs/reference/plot_counts-1.png

docs/reference/plot_counts.html

docs/reference/plot_image.html

docs/reference/pseudobulk_dim_plot-1.png

docs/reference/pseudobulk_dim_plot.html

docs/reference/pseudobulk_heatmap-1.png

docs/reference/pseudobulk_heatmap-2.png

docs/reference/pseudobulk_heatmap.html

docs/reference/pseudobulk_pca_plot-1.png

docs/reference/pseudobulk_pca_plot.html

docs/reference/pseudobulk_samples-1.png

docs/reference/pseudobulk_samples.html

docs/reference/show-STlist-method.html

docs/reference/spatial_metadata.html

docs/reference/summarize_STlist.html

docs/reference/summary-STlist-method.html

docs/reference/tissue_names.html

docs/reference/transform_data.html

docs/sitemap.xml

docs/smi_dir_structure.png

docs/spatialGE_workflow_v3.png

docs/spatial_gradients.png

inst/.DS_Store

inst/err.csv

logo.png

man/STclust.Rd man/STdiff.Rd man/STdiff_volcano.Rd man/STenrich.Rd man/STgradient.Rd man/SThet.Rd man/STlist-class.Rd man/STlist.Rd man/STplot.Rd man/STplot_interpolation.Rd man/compare_SThet.Rd man/dim-STlist-method.Rd man/distribution_plots.Rd man/filter_data.Rd man/gene_interpolation.Rd man/get_gene_meta.Rd man/load_images.Rd man/plot_counts.Rd man/plot_image.Rd man/pseudobulk_dim_plot.Rd man/pseudobulk_heatmap.Rd man/pseudobulk_samples.Rd man/show-STlist-method.Rd man/spatial_metadata.Rd man/summarize_STlist.Rd man/summary-STlist-method.Rd man/tissue_names.Rd man/transform_data.Rd

pkgdown/favicon/apple-touch-icon-120x120.png

pkgdown/favicon/apple-touch-icon-152x152.png

pkgdown/favicon/apple-touch-icon-180x180.png

pkgdown/favicon/apple-touch-icon-60x60.png

pkgdown/favicon/apple-touch-icon-76x76.png

pkgdown/favicon/apple-touch-icon.png

pkgdown/favicon/favicon-16x16.png

pkgdown/favicon/favicon-32x32.png

pkgdown/favicon/favicon.ico

spatialGE.Rproj

spatialGE_workflow_v3.png

src/RcppExports.cpp

src/seurat_helpers.cpp

src/spatialge_helpers.cpp

tests/testthat.R tests/testthat/test-tests.R vignettes/basic_functions_vignette.Rmd

vignettes/img/diagram_stenrich.png

vignettes/img/dir_structure.png

vignettes/img/metadata_file.png

vignettes/img/smi_dir_structure.png

vignettes/img/spatial_gradients.png

vignettes/spatial_differential_expression.Rmd vignettes/spatial_enrichment_gradients_smi.Rmd vignettes/troubleshooting.Rmd

vignettes/vignette_references.bib

FridleyLab/spatialGE documentation built on April 14, 2025, 9:37 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

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

Files in FridleyLab/spatialGE
Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in FridleyLab/spatialGE Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in FridleyLab/spatialGE
Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression