Files in patrickCNMartin/Vesalius
Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/pkgdown.yaml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/RcppExports.R R/cost.R R/data.R R/dispatch.R R/embeddings.R R/equalize_image.R R/global_bindings.R R/image_plot.R R/integration.R R/interoperability.R R/isolate_territories.R R/map_assays.R R/map_metrics.R R/misc.R R/morphology_operators.R R/multi_mod.R R/normalization.R R/object_modification.R R/object_utilities_and_methods.R R/objects.R R/progress_messages.R R/reformat.R R/regularize_image.R R/sanity_checks.R R/segment_image.R R/smooth_image.R R/spix.R R/territory_identity_and_markers.R R/territory_plot.R R/tiles.R R/vesalius.R R/view_gene_expression.R R/view_mapping_metrics.R README.md
_pkgdown.yml
data/vesalius.rda
inst/CITATION
inst/extdata/dentate.png
man/add_active_count_tag.Rd man/add_active_embedding_tag.Rd man/add_counts.Rd man/add_embeddings.Rd man/adjust_counts.Rd man/align_index.Rd man/assign_centers.Rd man/average_embed.Rd man/back_infer.Rd man/bubble_stack.Rd man/build_mapped_assay.Rd man/build_vesalius_assay.Rd man/calculate_scale.Rd man/cell_type_match.Rd man/check_barcodes.Rd man/check_binary_nature.Rd man/check_cells.Rd man/check_coordinates.Rd man/check_counts.Rd man/check_deg_method.Rd man/check_dim_selection_method.Rd man/check_embed_methods.Rd man/check_embedding_selection.Rd man/check_embeddings.Rd man/check_eq_method.Rd man/check_features.Rd man/check_for_zero_counts.Rd man/check_group_value.Rd man/check_image.Rd man/check_image_input.Rd man/check_inputs.Rd man/check_isolation_method.Rd man/check_min_spatial_index.Rd man/check_norm.Rd man/check_norm_methods.Rd man/check_segment_trial.Rd man/check_segmentation_method.Rd man/check_smoothing_kernel.Rd man/check_smoothing_level.Rd man/check_tensor_compression.Rd man/check_territory_trial.Rd man/check_tiles.Rd man/commit_log.Rd man/compute_effect_size.Rd man/compute_nearest_neighbor_graph.Rd man/concat_cost.Rd man/concat_embed.Rd man/concat_matches.Rd man/convexify.Rd man/coordinates.Rd man/counts.Rd man/create_alpha.Rd man/create_commit_log.Rd man/create_palette.Rd man/create_pseudo_centroids.Rd man/create_trial_tag.Rd man/detect_edges.Rd man/dispatch_batch.Rd man/dispatch_cost_groups.Rd man/dispatch_deg_group.Rd man/dispatch_sample.Rd man/dispatch_territory.Rd man/distance_pooling.Rd man/ecdf_eq.Rd man/embed_latent_space.Rd man/embed_lsi.Rd man/embed_lsi_umap.Rd man/embed_nmf.Rd man/embed_pca.Rd man/embed_pcal.Rd man/embed_umap.Rd man/equalize_image.Rd man/extend_boundary.Rd
man/figures/banner.png
man/filter_grid.Rd man/filter_maps.Rd man/filter_tiles.Rd man/format_c_to_ves.Rd man/format_call.Rd man/format_counts_for_deseq2.Rd man/format_counts_for_edger.Rd man/format_counts_for_logit.Rd man/format_ves_to_c.Rd man/future_ves_to_cimg.Rd man/generate_embeddings.Rd man/generate_spix.Rd man/generate_tiles.Rd man/get_active_count_tag.Rd man/get_active_embedding_tag.Rd man/get_assay_names.Rd man/get_coordinayes.Rd man/get_cost_contribution.Rd man/get_counts.Rd man/get_deg_metrics.Rd man/get_embeddings.Rd man/get_func_from_commit.Rd man/get_markers.Rd man/get_metric_clusters.Rd man/get_neighborhood_signal.Rd man/get_signal.Rd man/get_territories.Rd man/get_tiles.Rd man/globalise_territories.Rd man/graph_neighborhood.Rd man/graph_path_length.Rd man/hclust_scores.Rd man/identify_markers.Rd man/image_plot.Rd man/initialize_matches.Rd man/int_sctransform.Rd man/integrate_assays.Rd man/integrate_counts.Rd man/interlace_embeds.Rd man/internal_smooth.Rd man/isolate_territories.Rd man/jitter_coord.Rd man/jitter_counts.Rd man/joint_territories.Rd man/kmeans_segmentation.Rd man/knn_neighborhood.Rd man/layer_territory.Rd man/leiden_scores.Rd man/leiden_segmentation.Rd man/log_norm.Rd man/louvain_scores.Rd man/louvain_segmentation.Rd man/map_assays.Rd man/map_index.Rd man/match_cells.Rd man/merge_coordinates.Rd man/merge_territories.Rd man/message_switch.Rd man/min_max.Rd man/neighborhood_signal.Rd man/niche_composition.Rd man/no_norm.Rd man/norm_pixel.Rd man/optimize_matching.Rd man/overlap_distance_matrix.Rd man/pearson_approx.Rd man/point_mapping.Rd man/populate_graph.Rd man/process_counts.Rd man/radius_neighborhood.Rd man/rasterise.Rd man/rebalence_colors.Rd man/reduce_tensor_resolution.Rd man/regularise.Rd man/regularise_image.Rd man/rename_counts.Rd man/score_matches.Rd man/search_log.Rd man/segment_image.Rd man/select_initial_indices.Rd man/signal_similarity.Rd man/smooth_image.Rd man/summarise_territories.Rd man/territory_morphing.Rd man/territory_neighborhood.Rd man/territory_plot.Rd man/tfidf_norm.Rd man/unpack_territory_path.Rd man/update_matches.Rd man/update_vesalius_assay.Rd man/vesalius_assay-class.Rd man/vesalius_deg.Rd man/vesalius_deg_chisq.Rd man/vesalius_deg_deseq2.Rd man/vesalius_deg_edger.Rd man/vesalius_deg_fisher.Rd man/vesalius_deg_logit.Rd man/vesalius_deg_ttest.Rd man/vesalius_deg_wilcox.Rd man/vesalius_package.Rd man/view_gene_expression.Rd
src/RcppExports.cpp
src/cost.cpp
tests/testthat.R tests/testthat/helper-expectations.R tests/testthat/test_embeddings_and_tiles.R tests/testthat/test_image_processing.R tests/testthat/test_integration.R tests/testthat/test_mapping.R tests/testthat/test_mapping_metrics.R tests/testthat/test_misc.R tests/testthat/test_morphology_operators.R tests/testthat/test_territory_identity_and_markers.R tests/testthat/test_vesalius_objects.R tests/testthat/test_visualization.R vignettes/Vesalius_Analysis/Spatial_DNA_seq.Rmd vignettes/Vesalius_Analysis/Spatial_RNA_seq.Rmd vignettes/Vesalius_Analysis/Vesalius_MSB_analysis.Rmd vignettes/vesalius.Rmd
patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.