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
RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.