Files in LieberInstitute/spatialLIBD

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

.Rbuildignore

.github/.gitignore

.github/CODE_OF_CONDUCT.md .github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/feature_request_template.md .github/ISSUE_TEMPLATE/issue_template.md .github/SUPPORT.md

.github/workflows/check-bioc.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/add10xVisiumAnalysis.R R/add_images.R R/add_key.R R/annotate_registered_clusters.R R/app_server.R R/app_ui.R R/check_modeling_results.R R/check_sce.R R/check_sce_layer.R R/check_spe.R R/cluster_export.R R/cluster_import.R R/data.R R/enough_ram.R R/fetch_data.R R/frame_limits.R R/gene_set_enrichment.R R/gene_set_enrichment_plot.R R/geom_spatial.R R/get_colors.R R/img_edit.R R/img_update.R R/img_update_all.R R/layer_boxplot.R R/layer_matrix_plot.R R/layer_stat_cor.R R/layer_stat_cor_plot.R R/locate_images.R R/multi_gene_pca.R R/multi_gene_sparsity.R R/multi_gene_z_score.R R/read10xVisiumAnalysis.R R/read10xVisiumWrapper.R R/registration_block_cor.R R/registration_model.R R/registration_pseudobulk.R R/registration_stats_anova.R R/registration_stats_enrichment.R R/registration_stats_pairwise.R R/registration_wrapper.R R/run_app.R R/sce_to_spe.R R/sig_genes_extract.R R/sig_genes_extract_all.R R/sort_clusters.R R/spatialLIBD-package.R R/vis_clus.R R/vis_clus_p.R R/vis_gene.R R/vis_gene_p.R R/vis_grid_clus.R R/vis_grid_gene.R README.Rmd README.md

_pkgdown.yml

app.R

codecov.yml

data-raw/.gitignore

data-raw/asd_sfari_geneList.R

data-raw/asd_sfari_geneList.csv

data-raw/create_sce_example.R data-raw/create_spatialDLPFC_spe_subset.R data-raw/libd_layers_colors.R data-raw/logo.R data-raw/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.R

data-raw/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.csv

data/libd_layer_colors.rda

data/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.rda

dev/01_create_pkg.R dev/01_start.R dev/02_dev.R dev/02_git_github_setup.R dev/03_core_files.R dev/03_deploy.R dev/04_update.R dev/run_dev.R dev/shiny-server-files/error.Rmd

dev/shiny-server-files/error.html

dev/shiny-server-files/spatial_libd_subdomain/index.html

inst/CITATION

inst/app/www/README.md inst/app/www/documentation_sce_layer.md inst/app/www/documentation_spe.md

inst/app/www/favicon.ico

inst/app/www/footer.html

inst/extdata/SFARI-Gene_genes_01-03-2020release_02-04-2020export.csv

inst/extdata/metadata_Visium_SPG_AD.csv

inst/extdata/metadata_spatialDLPFC.csv

inst/extdata/metadata_spatialLIBD.csv

inst/scripts/make-data_spatialLIBD.R inst/scripts/make-metadata_Visium_SPG_AD.R inst/scripts/make-metadata_spatialDLPFC.R inst/scripts/make-metadata_spatialLIBD.R

inst/spe_wrapper_app/.gitignore

inst/spe_wrapper_app/app.R inst/spe_wrapper_app/deploy.R inst/spe_wrapper_app/www/README.md inst/spe_wrapper_app/www/documentation_sce_layer.md inst/spe_wrapper_app/www/documentation_spe.md

inst/spe_wrapper_app/www/favicon.ico

inst/spe_wrapper_app/www/footer.html

man/add10xVisiumAnalysis.Rd man/add_images.Rd man/add_key.Rd man/annotate_registered_clusters.Rd man/check_modeling_results.Rd man/check_sce.Rd man/check_sce_layer.Rd man/check_spe.Rd man/cluster_export.Rd man/cluster_import.Rd man/enough_ram.Rd man/fetch_data.Rd

man/figures/README-access_data-1.png

man/figures/logo.png

man/figures/paper_figure1.jpg

man/figures/spatial_registration.png

man/frame_limits.Rd man/gene_set_enrichment.Rd man/gene_set_enrichment_plot.Rd man/geom_spatial.Rd man/get_colors.Rd man/img_edit.Rd man/img_update.Rd man/img_update_all.Rd man/layer_boxplot.Rd man/layer_matrix_plot.Rd man/layer_stat_cor.Rd man/layer_stat_cor_plot.Rd man/libd_layer_colors.Rd man/locate_images.Rd man/multi_gene_pca.Rd man/multi_gene_sparsity.Rd man/multi_gene_z_score.Rd man/read10xVisiumAnalysis.Rd man/read10xVisiumWrapper.Rd man/registration_block_cor.Rd man/registration_model.Rd man/registration_pseudobulk.Rd man/registration_stats_anova.Rd man/registration_stats_enrichment.Rd man/registration_stats_pairwise.Rd man/registration_wrapper.Rd man/run_app.Rd man/sce_to_spe.Rd man/sig_genes_extract.Rd man/sig_genes_extract_all.Rd man/sort_clusters.Rd man/spatialLIBD-package.Rd man/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.Rd man/vis_clus.Rd man/vis_clus_p.Rd man/vis_gene.Rd man/vis_gene_p.Rd man/vis_grid_clus.Rd man/vis_grid_gene.Rd

pkgdown/extra.css

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

tests/testthat.R tests/testthat/test-ExperimentHub.R tests/testthat/test-gene_set_enrichment.R tests/testthat/test-multi_gene_pca.R tests/testthat/test-multi_gene_z_score.R tests/testthat/test-registration_model.R tests/testthat/test-registration_pseudobulk.R tests/testthat/test-registration_stats_anova.R tests/testthat/test-registration_stats_enrichment.R tests/testthat/test-vis_gene.R

vignettes/.gitignore

vignettes/TenX_data_download.Rmd vignettes/guide_to_spatial_registration.Rmd vignettes/multi_gene_plots.Rmd vignettes/spatialLIBD.Rmd

LieberInstitute/spatialLIBD documentation built on April 21, 2024, 6:47 p.m.