Files in RubD/Giotto_site
Spatial Single-Cell Transcriptomics Toolbox

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DESCRIPTION

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LICENSE

NAMESPACE

NEWS.Rmd NEWS.md R/NN_network.R R/auxiliary_giotto.R R/auxiliary_visuals.R R/clustering.R R/cross_section.R R/data.R R/differential_expression.R R/dimension_reduction.R R/general_help.R R/giotto.R R/giotto_viewer.R R/globals.R R/image_registration.R R/images.R R/interoperability.R R/python_environment.R R/python_hmrf.R R/spatial_enrichment.R R/spatial_genes.R R/spatial_interaction.R R/spatial_interaction_spot.R R/spatial_interaction_visuals.R R/spatial_structures.R R/spatial_visuals.R R/utilities.R R/utils-pipe.R R/variable_genes.R README.Rmd README.md

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index.Rmd index.md

inst/CITATION

inst/examples/mini_seqfish_test/mini_seqfish_v0.3.5_200529.R inst/examples/mini_starmap_test/mini_starmap_v0.3.5_200614.R inst/examples/mini_visium_test/mini_visium_deg_v0.3.5_200612.R

inst/extdata/datasets.txt

inst/extdata/deg_image.png

inst/extdata/deg_image2.png

inst/extdata/mouse_ligand_receptors.txt

inst/extdata/seqfish_field_expr.txt.gz

inst/extdata/seqfish_field_locs.txt

inst/extdata/sig_matrix.txt

inst/extdata/starmap_cell_loc.txt

inst/extdata/starmap_expr.txt.gz

inst/extdata/visium_DG_expr.txt.gz

inst/extdata/visium_DG_locs.txt

inst/faqs/giotto_installation/installation_issues.Rmd inst/faqs/giotto_installation/installation_issues.md

inst/howtos/giotto_images/vignette_1/1_a_spatplot.png

inst/howtos/giotto_images/vignette_1/1_b_spatplot_image.png

inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted.png

inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_1.png

inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_10.png

inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_2.png

inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_3.png

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inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_5.png

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inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_8.png

inst/howtos/giotto_images/vignette_1/1_c_spatplot_image_adjusted_9.png

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inst/howtos/giotto_images/vignette_1/3_a_external_image_negated.png

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inst/howtos/giotto_images/vignette_1/4_a_spatial_locations.png

inst/howtos/giotto_images/vignette_1/4_b_nr_genes.png

inst/howtos/giotto_images/vignette_1/4_c_nr_genes_black_bg.png

inst/howtos/giotto_images/vignette_1/4_d_nr_genes_charc_bg.png

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inst/howtos/giotto_images/vignette_1/5_b_PCA_reduction.png

inst/howtos/giotto_images/vignette_1/5_c_UMAP_reduction.png

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inst/howtos/giotto_images/vignette_1/7_a_covis_leiden_black.png

inst/howtos/giotto_images/vignette_1/7_b_covis_leiden_charc.png

inst/howtos/giotto_images/vignette_1/7_b_covis_leiden_negated.png

inst/howtos/giotto_images/vignette_1/8_a_spatgene_charc.png

inst/howtos/giotto_images/vignette_1/8_b_spatgene_charc_vor.png

inst/howtos/giotto_images/vignette_1/9_a_subset_spatgene_charc.png

inst/howtos/giotto_images/vignette_1/9_b_subset_spatgene_charc_vor.png

inst/howtos/instructions_and_plotting/instructions_and_plotting.Rmd inst/howtos/instructions_and_plotting/instructions_and_plotting.md

inst/howtos/instructions_and_plotting/vignette_1/original_clusters_black.png

inst/howtos/subset_giotto/subset_giotto.Rmd inst/howtos/subset_giotto/subset_giotto.md

inst/howtos/subset_giotto/vignette_1/1_whole_brain.png

inst/howtos/subset_giotto/vignette_1/2_whole_brain_clus4.png

inst/howtos/subset_giotto/vignette_1/3_whole_brain_clus4_noOther.png

inst/howtos/subset_giotto/vignette_1/4_whole_brain_by_group_leiden_1.png

inst/howtos/subset_giotto/vignette_1/4_whole_brain_by_group_leiden_2.png

inst/howtos/subset_giotto/vignette_1/5_whole_brain_HMRF.png

inst/howtos/subset_giotto/vignette_1/5_whole_brain_by_group_HMRF_1.png

inst/howtos/subset_giotto/vignette_1/5_whole_brain_by_group_HMRF_2.png

inst/howtos/subset_giotto/vignette_1/6_subset_brain.png

inst/howtos/subset_giotto/vignette_1/6_subset_brain_nr_genes.png

inst/howtos/subset_giotto/vignette_1/7_DG_loc_subset.png

inst/howtos/visualization_options/visualization_options.Rmd inst/howtos/visualization_options/visualization_options.md inst/howtos/voronoi_plots/howto_voronoi_plots.Rmd inst/howtos/voronoi_plots/howto_voronoi_plots.md

inst/howtos/voronoi_plots/vignette_1/1_voronoi.png

inst/howtos/voronoi_plots/vignette_1/2_voronoi_no_others.png

inst/howtos/voronoi_plots/vignette_1/3_voronoi_no_others_black_border.png

inst/howtos/voronoi_plots/vignette_1/4_voronoi_spat_dim.png

inst/howtos/voronoi_plots/vignette_1/5_voronoi_neighbors.png

inst/howtos/voronoi_plots/vignette_1/6_original_points.png

inst/howtos/voronoi_plots/vignette_1/7_voronoi_genes.png

inst/howtos/voronoi_plots/vignette_1/8_voronoi_gene_black_bg.png

inst/howtos/work_with_multiple_analyses/ppt_store_multiple_analyses2.png

inst/howtos/work_with_multiple_analyses/vignette_1/1_group_hvg.png

inst/howtos/work_with_multiple_analyses/vignette_1/1_hvg_table.png

inst/howtos/work_with_multiple_analyses/vignette_1/1_loess_hvg.png

inst/howtos/work_with_multiple_analyses/vignette_1/2_group_pca.png

inst/howtos/work_with_multiple_analyses/vignette_1/2_loess_pca.png

inst/howtos/work_with_multiple_analyses/vignette_1/3_group_umap.png

inst/howtos/work_with_multiple_analyses/vignette_1/3_loess_umap.png

inst/howtos/work_with_multiple_analyses/vignette_1/4_distance_network.png

inst/howtos/work_with_multiple_analyses/vignette_1/4_large_network.png

inst/howtos/work_with_multiple_analyses/vignette_1/4_spatial_network.png

inst/howtos/work_with_multiple_analyses/vignette_1/5_large_distance_network_genes.png

inst/howtos/work_with_multiple_analyses/vignette_1/5_large_network_genes.png

inst/howtos/work_with_multiple_analyses/work_with_multiple_analyses.Rmd inst/howtos/work_with_multiple_analyses/work_with_multiple_analyses.md

inst/images/general_figs/CODEX_spleen_image_summary.png

inst/images/general_figs/cortex_image_summary.png

inst/images/general_figs/cortex_svz_location_fields.png

inst/images/general_figs/cyCIF_PDAC_image_summary.png

inst/images/general_figs/cycif_paper_figure.png

inst/images/general_figs/diagram_giotto_workflow.png

inst/images/general_figs/merFISH_hypoth_image_summary.png

inst/images/general_figs/osmFISH_SS_cortex_image_summary.png

inst/images/general_figs/osmfish_image_demo.png

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inst/images/mouse_seqFISH_SS_cortex/vignette_200517/11_HMRF_2_k9_b.28.pdf

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inst/images/mouse_seqFISH_SS_cortex/vignette_200517/12_cell_cell_enrichment_sel_vs_not.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/12_cell_cell_enrichment_selected.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/12_heatmap_cell_cell_enrichment.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/12_network_cell_cell_enrichment.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/12_network_cell_cell_enrichment_self.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/12_network_cell_cell_enrichment_self.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/13_CPG_dotplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/13_ICG_barplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_communication_dotplot.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_communication_dotplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_communication_heatmap.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_expr_vs_spatial_activity.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_expr_vs_spatial_activity.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_expr_vs_spatial_activity_zoom.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_expr_vs_spatial_activity_zoom.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_spatial_recovery_activity.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/14_spatial_recovery_activity.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/2_spatial_locations.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/3_HVGplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/3_PCA_reduction.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/3_UMAP_reduction.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/3_screeplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/3_tSNE_reduction.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/4_UMAP_leiden.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/4_UMAP_leiden_subcluster.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/4_dendro.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/4_heatmap.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/5_covis_leiden.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/5_covis_leiden_selected.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/6_metaheatmap_gini.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/6_metaheatmap_scran.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/6_violinplot_gini.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/6_violinplot_scran.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_covisualization.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_covisualization2.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_covisualization_selection.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_heatmap.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_heatmap_selected.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_violinplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_violinplot_gini_paper.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/7_violinplot_gini_paper.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/8_grid.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/9_spatial_network_delaunay.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/9_spatial_network_dist.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/9_spatial_network_k10.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200517/9_spatial_network_k3.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/10_a_spatialgenes_km.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/10_b_spatialcoexpression_heatmap.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/10_c_spatialcoexpression_rank.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/10_d_spatialcoexpression_metagenes.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/11_HMRF_2_k9_b.28.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/12_a_barplot_cell_cell_enrichment.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/12_b_heatmap_cell_cell_enrichment.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/12_c_network_cell_cell_enrichment.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/12_d_network_cell_cell_enrichment_self.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/12_e_cell_cell_enrichment_selected.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/12_f_cell_cell_enrichment_sel_vs_not.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/13_a_CPG_dotplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/13_b_ICG_barplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_a_communication_dotplot.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_a_communication_dotplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_b_expr_vs_spatial_expression_rank.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_b_expr_vs_spatial_expression_rank.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_c_spatial_recovery_expression_rank.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_c_spatial_recovery_expression_rank.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_d_expr_vs_spatial_activity.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_d_expr_vs_spatial_activity.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_e_spatial_recovery_activity.pdf

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/14_e_spatial_recovery_activity.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/2_a_spatplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/3_a_HVGplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/3_b_screeplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/3_c_PCA_reduction.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/3_d_UMAP_reduction.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/3_e_tSNE_reduction.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/4_a_UMAP_leiden.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/4_b_UMAP_leiden_subcluster.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/4_c_heatmap.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/4_d_dendro.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/5_a_covis_leiden.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/5_b_covis_leiden_selected.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/6_a_violinplot_gini.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/6_b_metaheatmap_gini.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/7_a_violinplot.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/7_b_covisualization.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/7_c_heatmap.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/7_d_heatmap_selected.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/8_a_grid.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/9_a_spatial_network_delaunay.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/9_b_spatial_network_k3.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/9_c_spatial_network_k10.png

inst/images/mouse_seqFISH_SS_cortex/vignette_200914/9_d_spatial_network_dist.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/10_cluster_annotation_heatmap.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/11_dim_plot_detailed_cell_type.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/12_cell_type_co_vis.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/1_spatial_locations.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/2_hvg.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/3_pca_scree_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/4_umap.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/5_leiden_0.2.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/6_covisualize_leiden_0.2.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/7_heatmap_leiden_0.2.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/8_general_cell_type.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/9_cell_type_umap.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Ctgf_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Ctgf_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Cux2_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Cux2_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Pcp4_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Pcp4_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Rorb_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Rorb_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Slc17a7_cross_section_gene.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/Slc17a7_cross_section_gene3d.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/cross_section_spat.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/cross_section_spat3d.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/detailed_cell_types.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/insert_cross_section_Slc17a7.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/insert_cross_section_cell_types.png

inst/images/mouse_starmap_cortex/vignette_0.3.0/violinplot.png

inst/images/mouse_starmap_cortex/vignette_200917/10_cluster_annotation_heatmap.png

inst/images/mouse_starmap_cortex/vignette_200917/11_dim_plot_detailed_cell_type.png

inst/images/mouse_starmap_cortex/vignette_200917/12_cell_type_co_vis.png

inst/images/mouse_starmap_cortex/vignette_200917/1_spatial_locations.png

inst/images/mouse_starmap_cortex/vignette_200917/2_a_distribution_genes.png

inst/images/mouse_starmap_cortex/vignette_200917/2_b_distribution_cells.png

inst/images/mouse_starmap_cortex/vignette_200917/2_c_distribution_filters.png

inst/images/mouse_starmap_cortex/vignette_200917/2_hvg.png

inst/images/mouse_starmap_cortex/vignette_200917/3_b_signPCs.png

inst/images/mouse_starmap_cortex/vignette_200917/4_umap.png

inst/images/mouse_starmap_cortex/vignette_200917/5_leiden_0.2.png

inst/images/mouse_starmap_cortex/vignette_200917/6_a_violinplot.png

inst/images/mouse_starmap_cortex/vignette_200917/6_covisualize_leiden_0.2.png

inst/images/mouse_starmap_cortex/vignette_200917/7_heatmap_leiden_0.2.png

inst/images/mouse_starmap_cortex/vignette_200917/8_general_cell_type.png

inst/images/mouse_starmap_cortex/vignette_200917/9_cell_type_umap.png

inst/images/mouse_starmap_cortex/vignette_200917/Ctgf_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Ctgf_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Cux2_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Cux2_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Pcp4_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Pcp4_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Rorb_dim_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Rorb_spat_plot.png

inst/images/mouse_starmap_cortex/vignette_200917/Slc17a7_cross_section_gene.png

inst/images/mouse_starmap_cortex/vignette_200917/Slc17a7_cross_section_gene3d.png

inst/images/mouse_starmap_cortex/vignette_200917/cross_section_spat.png

inst/images/mouse_starmap_cortex/vignette_200917/cross_section_spat3d.png

inst/images/mouse_starmap_cortex/vignette_200917/detailed_cell_types.png

inst/images/mouse_starmap_cortex/vignette_200917/insert_cross_section_Slc17a7.png

inst/images/mouse_starmap_cortex/vignette_200917/insert_cross_section_cell_types.png

inst/images/mouse_starmap_cortex/vignette_200917/violinplot.png

inst/old_vignettes/cycif_pdac/human_cycif_PDAC_200601.Rmd inst/old_vignettes/osmfish_cortex/mouse_osmFISH_SScortex_200518.Rmd inst/old_vignettes/seqfish_cortex/mouse_seqFISH_cortex_200517.Rmd inst/old_vignettes/starmap_cortex/mouse_starmap_cortex.Rmd

inst/python/SpatialDE_wrapper.py

inst/python/get_result2.py

inst/python/python_leiden.py

inst/python/python_louvain.py

inst/python/python_spatial_genes.py

inst/python/reader.py

inst/python/reader2.py

inst/python/silhouette_rank_wrapper.py

inst/python/silhouette_rank_wrapper_v1.py

man/.Rapp.history

src/Giotto.so

src/processing.o

vignettes/.gitignore

vignettes/binder.Rmd vignettes/contribute.Rmd vignettes/docker.Rmd vignettes/faqs.Rmd vignettes/getting_started.Rmd vignettes/github_issues.Rmd vignettes/howto_giotto_class.Rmd vignettes/howto_images.Rmd vignettes/howto_voronoi_plots.Rmd vignettes/human_cycif_PDAC_200916.Rmd vignettes/installation_issues.Rmd vignettes/instructions_and_plotting.Rmd vignettes/metadata_and_subset_VC.Rmd vignettes/mini_seqfish.Rmd vignettes/mini_starmap.Rmd vignettes/mini_visium.Rmd vignettes/mouse_CODEX_spleen_200921.Rmd vignettes/mouse_merFISH_preoptic_region_200909.Rmd vignettes/mouse_osmFISH_SScortex_200915.Rmd vignettes/mouse_seqFISH_cortex_200914.Rmd vignettes/mouse_starmap_cortex_200917.Rmd vignettes/mouse_visium_brain_200918.Rmd vignettes/mouse_visium_brain_201226.Rmd vignettes/mouse_visium_kidney_200916.Rmd vignettes/subset_giotto.Rmd vignettes/tut0_giotto_environment.Rmd vignettes/tut10_giotto_spatcoexpression.Rmd vignettes/tut11_giotto_hmrf.Rmd vignettes/tut12_giotto_cell_interaction.Rmd vignettes/tut13_giotto_ICG.Rmd vignettes/tut14_giotto_signaling.Rmd vignettes/tut1_giotto_object.Rmd vignettes/tut2_giotto_object_process.Rmd vignettes/tut3_giotto_dim_reduction.Rmd vignettes/tut4_giotto_clustering.Rmd vignettes/tut5_giotto_markers.Rmd vignettes/tut6_giotto_annotation.Rmd vignettes/tut7_giotto_enrichment.Rmd vignettes/tut8_giotto_grid_network.Rmd vignettes/tut9_giotto_spatgenes.Rmd vignettes/visualization_options.Rmd vignettes/work_with_multiple_analyses.Rmd

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