Files in RubD/Giotto
Spatial Single-Cell Transcriptomics Toolbox
.Rbuildignore
.Rbuildignore.save
.github/workflows/main.yml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
Dockerfile
Giotto.Rproj
LICENSE
NAMESPACE
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
data/mini_giotto_3D.rda
data/mini_giotto_multi_cell.rda
data/mini_giotto_single_cell.rda
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/images/general_figs/overview_datasets.png
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
man/DT_removeNA.Rd
man/FSV_show.Rd
man/OR_test_fnc.Rd
man/PAGEEnrich.Rd
man/PAGE_DT_method.Rd
man/adapt_aspect_ratio.Rd
man/addCellIntMetadata.Rd
man/addCellMetadata.Rd
man/addCellStatistics.Rd
man/addGeneMetadata.Rd
man/addGeneStatistics.Rd
man/addGenesPerc.Rd
man/addGiottoImage.Rd
man/addGiottoImageToSpatPlot.Rd
man/addHMRF.Rd
man/addHMRF_V2.Rd
man/addNetworkLayout.Rd
man/addStatistics.Rd
man/adjustGiottoMatrix.Rd
man/aes_string2.Rd
man/all_plots_save_function.Rd
man/anndataToGiotto.Rd
man/annotateGiotto.Rd
man/annotateSpatialGrid.Rd
man/annotateSpatialNetwork.Rd
man/annotate_spatlocs_with_spatgrid_2D.Rd
man/annotate_spatlocs_with_spatgrid_3D.Rd
man/average_gene_gene_expression_in_groups.Rd
man/binSpect.Rd
man/binSpectMulti.Rd
man/binSpectSingle.Rd
man/cal_diff_per_interaction.Rd
man/cal_expr_residual.Rd
man/calc_spatial_enrichment_DT.Rd
man/calc_spatial_enrichment_matrix.Rd
man/calc_spatial_enrichment_minimum.Rd
man/calculateHVG.Rd
man/calculateMetaTable.Rd
man/calculateMetaTableCells.Rd
man/calculate_distance_and_weight.Rd
man/cellProximityBarplot.Rd
man/cellProximityEnrichment.Rd
man/cellProximityEnrichmentEachSpot.Rd
man/cellProximityEnrichmentSpots.Rd
man/cellProximityHeatmap.Rd
man/cellProximityNetwork.Rd
man/cellProximitySpatPlot.Rd
man/cellProximitySpatPlot2D.Rd
man/cellProximitySpatPlot3D.Rd
man/cellProximityVisPlot.Rd
man/cellProximityVisPlot_2D_ggplot.Rd
man/cellProximityVisPlot_2D_plotly.Rd
man/cellProximityVisPlot_3D_plotly.Rd
man/cell_proximity_spots.Rd
man/cell_proximity_spots_external.Rd
man/cell_proximity_spots_internal.Rd
man/changeGiottoInstructions.Rd
man/changeImageBg.Rd
man/checkAndFixSpatialGenes.Rd
man/checkGiottoEnvironment.Rd
man/chooseAvailableSpatialGenes.Rd
man/clusterCells.Rd
man/clusterSpatialCorGenes.Rd
man/cluster_enrich_analysis.Rd
man/colMeans_flex.Rd
man/colMeans_giotto.Rd
man/colSums_flex.Rd
man/colSums_giotto.Rd
man/combCCcom.Rd
man/combineCPG.Rd
man/combineCellProximityGenes.Rd
man/combineCellProximityGenes_per_interaction.Rd
man/combineICG.Rd
man/combineInteractionChangedGenes.Rd
man/combineMetadata.Rd
man/convertEnsemblToGeneSymbol.Rd
man/convert_mgImage_to_array_DT.Rd
man/convert_to_full_spatial_network.Rd
man/convert_to_reduced_spatial_network.Rd
man/cor_flex.Rd
man/cor_giotto.Rd
man/cor_sparse.Rd
man/createCrossSection.Rd
man/createGiottoImage.Rd
man/createGiottoInstructions.Rd
man/createGiottoObject.Rd
man/createGiottoVisiumObject.Rd
man/createHeatmap_DT.Rd
man/createMetagenes.Rd
man/createNearestNetwork.Rd
man/createRegZStackGobject.Rd
man/createSpatialDefaultGrid.Rd
man/createSpatialDelaunayNetwork.Rd
man/createSpatialEnrich.Rd
man/createSpatialGrid.Rd
man/createSpatialKNNnetwork.Rd
man/createSpatialNetwork.Rd
man/create_2d_mesh_grid_line_obj.Rd
man/create_KNNnetwork_dbscan.Rd
man/create_average_DT.Rd
man/create_average_detection_DT.Rd
man/create_cell_type_random_cell_IDs.Rd
man/create_cluster_matrix.Rd
man/create_crossSection_object.Rd
man/create_delaunayNetwork2D.Rd
man/create_delaunayNetwork3D.Rd
man/create_delaunayNetwork_RTriangle.Rd
man/create_delaunayNetwork_deldir.Rd
man/create_delaunayNetwork_geometry.Rd
man/create_delaunayNetwork_geometry_3D.Rd
man/create_dimObject.Rd
man/create_genes_to_use_matrix.Rd
man/create_jackstrawplot.Rd
man/create_mesh_grid_lines.Rd
man/create_screeplot.Rd
man/create_spatialGridObject.Rd
man/create_spatialGrid_default_2D.Rd
man/create_spatialGrid_default_3D.Rd
man/create_spatialNetworkObject.Rd
man/crossSectionGenePlot.Rd
man/crossSectionGenePlot3D.Rd
man/crossSectionPlot.Rd
man/crossSectionPlot3D.Rd
man/decide_cluster_order.Rd
man/detectSpatialCorGenes.Rd
man/detectSpatialPatterns.Rd
man/determine_cores.Rd
man/dimCellPlot.Rd
man/dimCellPlot2D.Rd
man/dimGenePlot.Rd
man/dimGenePlot2D.Rd
man/dimGenePlot3D.Rd
man/dimPlot.Rd
man/dimPlot2D.Rd
man/dimPlot2D_single.Rd
man/dimPlot3D.Rd
man/dimPlot_2D_plotly.Rd
man/dimPlot_3D_plotly.Rd
man/doHMRF.Rd
man/doHMRF_V2.Rd
man/doHclust.Rd
man/doKmeans.Rd
man/doLeidenCluster.Rd
man/doLeidenSubCluster.Rd
man/doLouvainCluster.Rd
man/doLouvainCluster_community.Rd
man/doLouvainCluster_multinet.Rd
man/doLouvainSubCluster.Rd
man/doLouvainSubCluster_community.Rd
man/doLouvainSubCluster_multinet.Rd
man/doRandomWalkCluster.Rd
man/doSNNCluster.Rd
man/do_cell_proximity_test.Rd
man/do_cell_proximity_test_spot.Rd
man/do_limmatest.Rd
man/do_multi_permuttest_random.Rd
man/do_multi_permuttest_random_spot.Rd
man/do_page_permutation.Rd
man/do_permuttest_original.Rd
man/do_permuttest_original_spot.Rd
man/do_permuttest_random.Rd
man/do_permuttest_random_spot.Rd
man/do_permuttest_spot.Rd
man/do_rank_permutation.Rd
man/do_spatial_grid_averaging.Rd
man/do_spatial_knn_smoothing.Rd
man/do_ttest.Rd
man/do_wilctest.Rd
man/dt_to_matrix.Rd
man/enrich_analysis.Rd
man/enrich_deconvolution.Rd
man/estimateCellCellDistance.Rd
man/estimateImageBg.Rd
man/evaluate_expr_matrix.Rd
man/evaluate_spatial_locations.Rd
man/explainGiottoInstructions.Rd
man/exportGiottoViewer.Rd
man/exprCellCellcom.Rd
man/extend_vector.Rd
man/extended_gini_fun.Rd
man/extractNearestNetwork.Rd
man/fDataDT.Rd
man/filterCPG.Rd
man/filterCellProximityGenes.Rd
man/filterCombinations.Rd
man/filterDistributions.Rd
man/filterGiotto.Rd
man/filterICG.Rd
man/filterICGSpot.Rd
man/filterInteractionChangedGenes.Rd
man/filterSpatialGenes.Rd
man/filter_network.Rd
man/findCPG.Rd
man/findCellProximityGenes.Rd
man/findCellProximityGenes_per_interaction.Rd
man/findGiniMarkers.Rd
man/findGiniMarkers_one_vs_all.Rd
man/findICG.Rd
man/findICGSpot.Rd
man/findICG_per_interaction_spot.Rd
man/findInteractionChangedGenes.Rd
man/findMarkers.Rd
man/findMarkers_one_vs_all.Rd
man/findMastMarkers.Rd
man/findMastMarkers_one_vs_all.Rd
man/findNetworkNeighbors.Rd
man/findScranMarkers.Rd
man/findScranMarkers_one_vs_all.Rd
man/find_dampening_constant.Rd
man/find_grid_2D.Rd
man/find_grid_3D.Rd
man/find_grid_x.Rd
man/find_grid_y.Rd
man/find_grid_z.Rd
man/find_x_y_ranges.Rd
man/flex_lapply.Rd
man/geneExpDWLS.Rd
man/general_save_function.Rd
man/get10Xmatrix.Rd
man/get10Xmatrix_h5.Rd
man/getClusterSimilarity.Rd
man/getDendrogramSplits.Rd
man/getDistinctColors.Rd
man/getGiottoImage.Rd
man/getSpatialDataset.Rd
man/get_cross_section_coordinates.Rd
man/get_distance.Rd
man/get_os.Rd
man/get_sectionThickness.Rd
man/ggplot_save_function.Rd
man/giotto-class.Rd
man/giotto_lapply.Rd
man/heatmSpatialCorGenes.Rd
man/hyperGeometricEnrich.Rd
man/initHMRF_V2.Rd
man/insertCrossSectionGenePlot3D.Rd
man/insertCrossSectionSpatPlot3D.Rd
man/installGiottoEnvironment.Rd
man/install_giotto_environment.Rd
man/install_giotto_environment_specific.Rd
man/jackstrawPlot.Rd
man/join_expression.Rd
man/kmeans_arma_binarize.Rd
man/kmeans_arma_subset_binarize.Rd
man/kmeans_binarize.Rd
man/kmeans_binarize_wrapper.Rd
man/lapply_flex.Rd
man/libNorm_giotto.Rd
man/loadHMRF.Rd
man/logNorm_giotto.Rd
man/makeSignMatrixDWLS.Rd
man/makeSignMatrixDWLSfromMatrix.Rd
man/makeSignMatrixPAGE.Rd
man/makeSignMatrixRank.Rd
man/make_simulated_network.Rd
man/mean_expr_det_test.Rd
man/mean_flex.Rd
man/mean_giotto.Rd
man/mergeClusters.Rd
man/mini_giotto_3D.Rd
man/mini_giotto_multi_cell.Rd
man/mini_giotto_single_cell.Rd
man/my_arowMeans.Rd
man/my_growMeans.Rd
man/my_rowMeans.Rd
man/mygini_fun.Rd
man/nnDT_to_kNN.Rd
man/node_clusters.Rd
man/normalizeGiotto.Rd
man/numPts_below_line.Rd
man/optimize_deconvolute_dwls.Rd
man/optimize_solveDampenedWLS.Rd
man/pDataDT.Rd
man/package_check.Rd
man/pca_giotto.Rd
man/pipe.Rd
man/plotCCcomDotplot.Rd
man/plotCCcomHeatmap.Rd
man/plotCPG.Rd
man/plotCellProximityGenes.Rd
man/plotCellProximityGenesSpot.Rd
man/plotCombineCCcom.Rd
man/plotCombineCPG.Rd
man/plotCombineCellCellCommunication.Rd
man/plotCombineCellProximityGenes.Rd
man/plotCombineICG.Rd
man/plotCombineInteractionChangedGenes.Rd
man/plotGiottoImage.Rd
man/plotHeatmap.Rd
man/plotICG.Rd
man/plotICGSpot.Rd
man/plotInteractionChangedGenes.Rd
man/plotMetaDataCellsHeatmap.Rd
man/plotMetaDataHeatmap.Rd
man/plotPCA.Rd
man/plotPCA_2D.Rd
man/plotPCA_3D.Rd
man/plotRankSpatvsExpr.Rd
man/plotRecovery.Rd
man/plotRecovery_sub.Rd
man/plotStatDelaunayNetwork.Rd
man/plotTSNE.Rd
man/plotTSNE_2D.Rd
man/plotTSNE_3D.Rd
man/plotUMAP.Rd
man/plotUMAP_2D.Rd
man/plotUMAP_3D.Rd
man/plot_network_layer_ggplot.Rd
man/plot_point_layer_ggplot.Rd
man/plot_point_layer_ggplot_noFILL.Rd
man/plot_spat_image_layer_ggplot.Rd
man/plot_spat_point_layer_ggplot.Rd
man/plot_spat_point_layer_ggplot_noFILL.Rd
man/plot_spat_scatterpie_layer_ggplot.Rd
man/plot_spat_voronoi_layer_ggplot.Rd
man/plotly_axis_scale_2D.Rd
man/plotly_axis_scale_3D.Rd
man/plotly_grid.Rd
man/plotly_network.Rd
man/processGiotto.Rd
man/projection_fun.Rd
man/rankEnrich.Rd
man/rankSpatialCorGroups.Rd
man/rank_binarize.Rd
man/readExprMatrix.Rd
man/readGiottoInstructions.Rd
man/read_crossSection.Rd
man/register_spatial_locations.Rd
man/removeCellAnnotation.Rd
man/removeGeneAnnotation.Rd
man/removeGiottoEnvironment.Rd
man/replaceGiottoInstructions.Rd
man/reshape_to_data_point.Rd
man/reshape_to_mesh_grid_obj.Rd
man/return_giotto_environment_path.Rd
man/return_giotto_environment_path_executable.Rd
man/rotate_spatial_locations.Rd
man/rowMeans_flex.Rd
man/rowMeans_giotto.Rd
man/rowSums_flex.Rd
man/rowSums_giotto.Rd
man/runDWLSDeconv.Rd
man/runHyperGeometricEnrich.Rd
man/runPAGEEnrich.Rd
man/runPAGEEnrich_OLD.Rd
man/runPCA.Rd
man/runPCA_factominer.Rd
man/runPCA_prcomp_irlba.Rd
man/runPatternSimulation.Rd
man/runRankEnrich.Rd
man/runSpatialDeconv.Rd
man/runSpatialEnrich.Rd
man/runUMAP.Rd
man/run_spatial_sim_tests_multi.Rd
man/run_spatial_sim_tests_one_rep.Rd
man/runtSNE.Rd
man/sampling_sp_genes.Rd
man/scale_spatial_locations.Rd
man/screePlot.Rd
man/selectPatternGenes.Rd
man/select_NearestNetwork.Rd
man/select_dimReduction.Rd
man/select_expression_values.Rd
man/select_spatialGrid.Rd
man/select_spatialNetwork.Rd
man/set_giotto_python_path.Rd
man/show-methods.Rd
man/showClusterDendrogram.Rd
man/showClusterHeatmap.Rd
man/showGiottoImageNames.Rd
man/showGiottoInstructions.Rd
man/showGrids.Rd
man/showNetworks.Rd
man/showPattern.Rd
man/showPattern2D.Rd
man/showPattern3D.Rd
man/showPatternGenes.Rd
man/showProcessingSteps.Rd
man/showSaveParameters.Rd
man/showSpatialCorGenes.Rd
man/signPCA.Rd
man/silhouetteRank.Rd
man/silhouetteRankTest.Rd
man/simulateOneGenePatternGiottoObject.Rd
man/solve_OLS_internal.Rd
man/solve_dampened_WLSj.Rd
man/sort_combine_two_DT_columns.Rd
man/spark.Rd
man/spatCellCellcom.Rd
man/spatCellCellcomSpots.Rd
man/spatCellPlot.Rd
man/spatCellPlot2D.Rd
man/spatDeconvPlot.Rd
man/spatDimCellPlot.Rd
man/spatDimCellPlot2D.Rd
man/spatDimGenePlot.Rd
man/spatDimGenePlot2D.Rd
man/spatDimGenePlot3D.Rd
man/spatDimPlot.Rd
man/spatDimPlot2D.Rd
man/spatDimPlot3D.Rd
man/spatGenePlot.Rd
man/spatGenePlot2D.Rd
man/spatGenePlot3D.Rd
man/spatNetwDistributions.Rd
man/spatNetwDistributionsDistance.Rd
man/spatNetwDistributionsKneighbors.Rd
man/spatPlot.Rd
man/spatPlot2D.Rd
man/spatPlot2D_single.Rd
man/spatPlot3D.Rd
man/spatPlot_2D_plotly.Rd
man/spatPlot_3D_plotly.Rd
man/spat_OR_func.Rd
man/spat_OR_func_DT.Rd
man/spat_fish_func.Rd
man/spat_fish_func_DT.Rd
man/spatialAEH.Rd
man/spatialDE.Rd
man/specificCellCellcommunicationScores.Rd
man/specific_CCCScores_spots.Rd
man/split_dendrogram_in_two.Rd
man/spot_deconvolution.Rd
man/stack_spatlocs.Rd
man/standardise_flex.Rd
man/standardise_giotto.Rd
man/stitchFieldCoordinates.Rd
man/stitchTileCoordinates.Rd
man/subClusterCells.Rd
man/subsetGiotto.Rd
man/subsetGiottoLocs.Rd
man/t_flex.Rd
man/t_giotto.Rd
man/trakem2_rigid_transf_extract.Rd
man/transform_2d_mesh_to_3d_mesh.Rd
man/trendSceek.Rd
man/updateGiottoImage.Rd
man/viewHMRFresults.Rd
man/viewHMRFresults2D.Rd
man/viewHMRFresults3D.Rd
man/viewHMRFresults_V2.Rd
man/violinPlot.Rd
man/writeHMRFresults.Rd
man/write_giotto_viewer_annotation.Rd
man/write_giotto_viewer_dim_reduction.Rd
man/write_giotto_viewer_numeric_annotation.Rd
man/xy_translate_spatial_locations.Rd
src/RcppExports.o
src/processing.o
vignettes/.gitignore
vignettes/mini_seqfish.Rmd
vignettes/mini_starmap.Rmd
vignettes/mini_visium.Rmd
