Files in RubD/Giotto
Spatial single-cell transcriptomics pipeline.

.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
Giotto.Rproj
Giotto_0.1.2.pdf
LICENSE
LICENSE.md
NAMESPACE
R/NN_network.R
R/auxiliary.R
R/auxiliary_giotto.R R/auxiliary_visuals.R R/clustering.R R/differential_expression.R R/dimension_reduction.R R/general_help.R R/giotto.R R/giotto_viewer.R R/python_hmrf.R R/spatial_genes.R R/spatial_interaction.R R/spatial_interaction_visuals.R R/spatial_structures.R R/spatial_visuals.R R/utils-pipe.R R/variable_genes.R README.Rmd README.md
inst/.DS_Store
inst/examples/.DS_Store
inst/examples/mouse_cortex_svz/.DS_Store
inst/examples/mouse_cortex_svz/cell_cell_neighbors.png
inst/examples/mouse_cortex_svz/cortex_svz_location_fields.png
inst/examples/mouse_cortex_svz/double_gene_enrichment.png
inst/examples/mouse_cortex_svz/man/.DS_Store
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inst/examples/mouse_cortex_svz/man/figures/README-unnamed-chunk-10-2.png
inst/examples/mouse_cortex_svz/man/figures/README-unnamed-chunk-10-3.png
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inst/examples/mouse_cortex_svz/mouse_cortex_1_simple.Rmd inst/examples/mouse_cortex_svz/mouse_cortex_1_simple.md inst/examples/mouse_cortex_svz/mouse_cortex_1_simple_improved.Rmd inst/examples/mouse_cortex_svz/mouse_cortex_1_simple_improved.md inst/examples/mouse_cortex_svz/mouse_cortex_example.Rmd inst/examples/mouse_cortex_svz/mouse_cortex_example.md inst/examples/mouse_cortex_svz/mouse_cortex_example.pdf
inst/examples/mouse_cortex_svz/mouse_cortex_example_test.html
inst/examples/mouse_cortex_svz/seqfish_cortex_Giotto_v0.1.2.Rmd inst/examples/mouse_cortex_svz/seqfish_cortex_Giotto_v0.1.2.md
inst/examples/mouse_cortex_svz/single_gene_enrichemt.png
inst/examples/mouse_olfactory_bulb/OB_location_fields.png
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inst/examples/mouse_olfactory_bulb/mouse_olfactory_bulb_example.Rmd inst/examples/mouse_olfactory_bulb/mouse_olfactory_bulb_example.md
inst/examples/mouse_osmFISH_SS_cortex/.DS_Store
inst/examples/mouse_osmFISH_SS_cortex/cell_cell_neighbors.png
inst/examples/mouse_osmFISH_SS_cortex/double_gene_enrichment.png
inst/examples/mouse_osmFISH_SS_cortex/figures/.DS_Store
inst/examples/mouse_osmFISH_SS_cortex/figures/10_final_hmrf_b0.5.png
inst/examples/mouse_osmFISH_SS_cortex/figures/10_final_hmrf_b0.png
inst/examples/mouse_osmFISH_SS_cortex/figures/11_barplot_cell_cell_enrichment.png
inst/examples/mouse_osmFISH_SS_cortex/figures/11_cell_cell_enrichment_selected.png
inst/examples/mouse_osmFISH_SS_cortex/figures/11_heatmap_cell_cell_enrichment.png
inst/examples/mouse_osmFISH_SS_cortex/figures/11_network_cell_cell_enrichment.png
inst/examples/mouse_osmFISH_SS_cortex/figures/1_original_clusters.png
inst/examples/mouse_osmFISH_SS_cortex/figures/1_original_regions.png
inst/examples/mouse_osmFISH_SS_cortex/figures/2_PCA_reduction.png
inst/examples/mouse_osmFISH_SS_cortex/figures/2_PCA_screeplot.png
inst/examples/mouse_osmFISH_SS_cortex/figures/2_UMAP_reduction.png
inst/examples/mouse_osmFISH_SS_cortex/figures/2_tSNE_reduction.png
inst/examples/mouse_osmFISH_SS_cortex/figures/3_UMAP_hclust.png
inst/examples/mouse_osmFISH_SS_cortex/figures/3_UMAP_kmeans.png
inst/examples/mouse_osmFISH_SS_cortex/figures/3_UMAP_leiden.png
inst/examples/mouse_osmFISH_SS_cortex/figures/3_UMAP_leiden_merged.png
inst/examples/mouse_osmFISH_SS_cortex/figures/3_leiden_merged_dendrogram.png
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inst/examples/mouse_osmFISH_SS_cortex/figures/4_covis_leiden_merged.png
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inst/examples/mouse_osmFISH_SS_cortex/figures/5_cluster_heatmap_leiden_merged.png
inst/examples/mouse_osmFISH_SS_cortex/figures/5_violinplot_leiden_merged.png
inst/examples/mouse_osmFISH_SS_cortex/figures/6_annotation_leiden_merged_coarse.png
inst/examples/mouse_osmFISH_SS_cortex/figures/6_annotation_leiden_merged_detailed.png
inst/examples/mouse_osmFISH_SS_cortex/figures/6_annotation_leiden_merged_first.png
inst/examples/mouse_osmFISH_SS_cortex/figures/7_grid_det_cell_types.png
inst/examples/mouse_osmFISH_SS_cortex/figures/7_pattern1_pca.png
inst/examples/mouse_osmFISH_SS_cortex/figures/7_pattern1_pca_genes.png
inst/examples/mouse_osmFISH_SS_cortex/figures/7_pattern3_pca.png
inst/examples/mouse_osmFISH_SS_cortex/figures/7_pattern3_pca_genes.png
inst/examples/mouse_osmFISH_SS_cortex/figures/8_spatial_network_k5.png
inst/examples/mouse_osmFISH_SS_cortex/figures/9_spatial_network_k5_genes.png
inst/examples/mouse_osmFISH_SS_cortex/osmFISH_SS_cortex_Giotto_v0.1.2.Rmd inst/examples/mouse_osmFISH_SS_cortex/osmFISH_SS_cortex_Giotto_v0.1.2.md
inst/examples/mouse_osmFISH_SS_cortex/osmFISH_data.png
inst/examples/mouse_osmFISH_SS_cortex/single_gene_enrichemt.png
inst/examples/mouse_slideseq_cerebellum/.DS_Store
inst/examples/mouse_slideseq_cerebellum/cell_cell_neighbors.png
inst/examples/mouse_slideseq_cerebellum/double_gene_enrichment.png
inst/examples/mouse_slideseq_cerebellum/figures/.DS_Store
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inst/examples/mouse_slideseq_cerebellum/figures/10_cell_cell_enrichment_selected.png
inst/examples/mouse_slideseq_cerebellum/figures/10_heatmap_cell_cell_enrichment.png
inst/examples/mouse_slideseq_cerebellum/figures/10_network_cell_cell_enrichment.png
inst/examples/mouse_slideseq_cerebellum/figures/1_after_filter.png
inst/examples/mouse_slideseq_cerebellum/figures/1_before_filter.png
inst/examples/mouse_slideseq_cerebellum/figures/2_PCA_reduction.png
inst/examples/mouse_slideseq_cerebellum/figures/2_PCA_screeplot.png
inst/examples/mouse_slideseq_cerebellum/figures/2_UMAP_reduction.png
inst/examples/mouse_slideseq_cerebellum/figures/3_UMAP_leiden.png
inst/examples/mouse_slideseq_cerebellum/figures/3_dendrogram_leiden_clusters.png
inst/examples/mouse_slideseq_cerebellum/figures/3_heatmap_leiden_clusters.png
inst/examples/mouse_slideseq_cerebellum/figures/4_covisual_leiden.png
inst/examples/mouse_slideseq_cerebellum/figures/5_DEG_heatmap_clusters.png
inst/examples/mouse_slideseq_cerebellum/figures/6_annotation_cell_types.png
inst/examples/mouse_slideseq_cerebellum/figures/6_annotation_cell_types_Granule.png
inst/examples/mouse_slideseq_cerebellum/figures/6_annotation_cell_types_Oligo.png
inst/examples/mouse_slideseq_cerebellum/figures/6_annotation_cell_types_Purkinje.png
inst/examples/mouse_slideseq_cerebellum/figures/7_grid_det_cell_types.png
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inst/examples/mouse_slideseq_cerebellum/figures/7_pattern1_pca_genes.png
inst/examples/mouse_slideseq_cerebellum/figures/7_pattern2_pca.png
inst/examples/mouse_slideseq_cerebellum/figures/7_pattern2_pca_genes.png
inst/examples/mouse_slideseq_cerebellum/figures/8_spatial_network_k5.png
inst/examples/mouse_slideseq_cerebellum/figures/8_spatial_network_k5_restricted.png
inst/examples/mouse_slideseq_cerebellum/figures/9_spatial_network_k5_genes.png
inst/examples/mouse_slideseq_cerebellum/single_gene_enrichemt.png
inst/examples/mouse_slideseq_cerebellum/slideseq_cerebellum_Giotto_v0.1.2.Rmd inst/examples/mouse_slideseq_cerebellum/slideseq_cerebellum_Giotto_v0.1.2.md
inst/examples/mouse_slideseq_cerebellum/slideseq_data_cerebellum.png
inst/examples/mouse_starmap_cortex/.DS_Store
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inst/examples/mouse_starmap_cortex/figures/10_hmrf_b0.png
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inst/examples/mouse_starmap_cortex/figures/DEG_heatmap_cells.png
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inst/examples/mouse_starmap_cortex/single_gene_enrichemt.png
inst/examples/mouse_starmap_cortex/starmap_3D_data.png
inst/examples/mouse_starmap_cortex/starmap_cortex_Giotto_v0.1.2.Rmd inst/examples/mouse_starmap_cortex/starmap_cortex_Giotto_v0.1.2.md
inst/extdata/.DS_Store
inst/extdata/OB_centroids.csv
inst/extdata/OB_expression.txt
inst/extdata/OB_location_fields.png
inst/extdata/OB_metadata.txt
inst/extdata/cortex_annotation.txt
inst/extdata/cortex_fields_info.txt
inst/extdata/cortex_svz_centroids_rotated.csv
inst/extdata/cortex_svz_expression.txt
inst/extdata/cortex_svz_location_fields.png
inst/extdata/mouse_ligand_receptors.txt
inst/faqs/.DS_Store
inst/faqs/metadata_and_subset/.DS_Store
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inst/faqs/metadata_and_subset/man/figures/README-unnamed-chunk-9-1.png
inst/faqs/metadata_and_subset/metadata_and_subset_VC.Rmd inst/faqs/metadata_and_subset/metadata_and_subset_VC.md
inst/images/.DS_Store
inst/images/OB_image_summary.png
inst/images/cortex_image_summary.png
inst/images/osmFISH_SS_cortex_image_summary.png
inst/images/slideseq_cerebellum_image_summary.png
inst/images/starmap_cortex_image_summary.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/python_spatial_genes_old_v1.py
inst/python/python_spatial_genes_old_v2.py
inst/python/python_spatial_genes_old_v3.py
inst/python/reader.py
inst/python/reader_old_v1.py
inst/python/reader_old_v2.py
man/.Rapp.history
man/FSV_show.Rd man/GenePattern_show.Rd man/OR_function2.Rd man/Spatial_AEH.Rd man/Spatial_DE.Rd man/addCellMetadata.Rd man/addCellStatistics.Rd man/addGeneMetadata.Rd man/addGeneStatistics.Rd man/addHMRF.Rd man/addNetworkLayout.Rd man/addStatistics.Rd man/adjustGiottoMatrix.Rd man/allCellCellcommunicationsScores.Rd man/annotateGiotto.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/binGetSpatialGenes.Rd man/calculateHVG.Rd man/calculateMetaTable.Rd man/calculateSpatialGenes.Rd man/calculate_spatial_genes_python.Rd man/cellProximityBarplot.Rd man/cellProximityEnrichment.Rd man/cellProximityHeatmap.Rd man/cellProximityNetwork.Rd man/cellProximityVisPlot.Rd man/cellProximityVisPlot_2D_ggplot.Rd man/cellProximityVisPlot_2D_plotly.Rd man/cellProximityVisPlot_3D_plotly.Rd man/changeGiottoInstructions.Rd man/clusterCells.Rd man/createGiottoInstructions.Rd man/createGiottoObject.Rd man/createHeatmap_DT.Rd man/createNearestNetwork.Rd man/createSpatialGrid.Rd man/createSpatialGrid_2D.Rd man/createSpatialGrid_3D.Rd man/createSpatialNetwork.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_dimObject.Rd man/decide_cluster_order.Rd man/detectSpatialPatterns.Rd man/dimGenePlot2D.Rd man/dimPlot2D.Rd man/direction_test_CPG.Rd man/doHMRF.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/dt_to_matrix.Rd man/exportGiottoViewer.Rd man/exprOnlyCellCellcommunicationScores.Rd man/extended_gini_fun.Rd man/extractNearestNetwork.Rd man/fDataDT.Rd man/filterCombinations.Rd man/filterDistributions.Rd man/filterGiotto.Rd man/findGiniMarkers.Rd man/findGiniMarkers_one_vs_all.Rd man/findMarkers.Rd man/findMarkers_one_vs_all.Rd man/findMastMarkers.Rd man/findMastMarkers_one_vs_all.Rd man/findScranMarkers.Rd man/findScranMarkers_one_vs_all.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/fish_function.Rd man/fish_function2.Rd man/getCellProximityGeneScores.Rd man/getClusterSimilarity.Rd man/getDendrogramSplits.Rd man/getDistinctColors.Rd man/getGeneToGeneSelection.Rd man/get_cell_to_cell_sorted_name_conversion.Rd man/get_interaction_gene_enrichment.Rd man/get_specific_interaction_gene_enrichment.Rd man/ggplot_save_function.Rd man/giotto-class.Rd man/iterCluster.Rd man/iterLeidenCluster.Rd man/iterLouvainCluster.Rd man/iterLouvainCluster_community.Rd man/iterLouvainCluster_multinet.Rd man/kmeans_binarize.Rd man/loadHMRF.Rd man/make_simulated_network.Rd man/mergeClusters.Rd man/mygini_fun.Rd man/nnDT_to_kNN.Rd man/node_clusters.Rd man/normalizeGiotto.Rd man/pDataDT.Rd man/pipe.Rd man/plotCPGscores.Rd man/plotGTGscores.Rd man/plotHeatmap.Rd man/plotMetaDataHeatmap.Rd man/plotPCA.Rd man/plotPCA_2D.Rd man/plotTSNE.Rd man/plotTSNE_2D.Rd man/plotUMAP.Rd man/plotUMAP_2D.Rd man/plot_network_layer_ggplot.Rd man/plot_point_layer_ggplot.Rd man/plot_spat_point_layer_ggplot.Rd man/plotly_axis_scale_2D.Rd man/plotly_axis_scale_3D.Rd man/plotly_grid.Rd man/plotly_network.Rd man/print.giotto.Rd man/rank_binarize.Rd man/readGiottoInstructions.Rd man/removeCellAnnotation.Rd man/removeGeneAnnotation.Rd man/runPCA.Rd man/runUMAP.Rd man/runtSNE.Rd man/selectPatternGenes.Rd man/select_expression_values.Rd man/show-giotto-method.Rd man/showCPGscores.Rd man/showClusterDendrogram.Rd man/showClusterHeatmap.Rd man/showGTGscores.Rd man/showGeneExpressionProximityScore.Rd man/showGiottoInstructions.Rd man/showIntExpressionProximityScore.Rd man/showPattern.Rd man/showPatternGenes.Rd man/showProcessingSteps.Rd man/showTopGeneToGene.Rd man/signPCA.Rd man/spatDimGenePlot2D.Rd man/spatDimPlot2D.Rd man/spatGenePlot2D.Rd man/spatPlot2D.Rd man/specificCellCellcommunicationScores.Rd man/split_dendrogram_in_two.Rd man/stitchFieldCoordinates.Rd man/subClusterCells.Rd man/subsetGiotto.Rd man/viewHMRFresults.Rd man/violinPlot.Rd man/visDimGenePlot.Rd man/visDimGenePlot_2D_ggplot.Rd man/visDimGenePlot_3D_plotly.Rd man/visDimPlot.Rd man/visDimPlot_2D_ggplot.Rd man/visDimPlot_2D_plotly.Rd man/visDimPlot_3D_plotly.Rd man/visForceLayoutPlot.Rd man/visGenePlot.Rd man/visGenePlot_2D_ggplot.Rd man/visGenePlot_3D_plotly.Rd man/visPlot.Rd man/visPlot_2D_ggplot.Rd man/visPlot_2D_plotly.Rd man/visPlot_3D_plotly.Rd man/visSpatDimGenePlot.Rd man/visSpatDimGenePlot_2D.Rd man/visSpatDimGenePlot_3D.Rd man/visSpatDimPlot.Rd man/visSpatDimPlot_2D.Rd man/visSpatDimPlot_3D.Rd man/writeHMRFresults.Rd man/write_giotto_viewer_annotation.Rd man/write_giotto_viewer_dim_reduction.Rd
vignettes/.DS_Store
vignettes/.gitignore
vignettes/mouse_cortex_vignette.Rmd
RubD/Giotto documentation built on Nov. 16, 2019, 1:18 a.m.