Files in drieslab/Giotto_site_suite
Spatial Single-Cell Transcriptomics Toolbox

.Rbuildignore

.Rbuildignore.save

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md

.github/workflows/R-CMD-check.yaml

.gitignore

CODE_OF_CONDUCT.md

DESCRIPTION

LICENSE.md

NAMESPACE

NEWS.md R/NN_network.R R/accessors.R R/auxiliary_giotto.R R/auxiliary_visuals.R R/cell_segmentation.R R/classes.R R/clustering.R R/convenience.R R/cross_section.R R/data_evaluation.R R/data_input.R R/dd.R R/differential_expression.R R/dimension_reduction.R R/general_help.R R/generics.R R/giotto.R R/giotto_structures.R R/giotto_viewer.R R/globals.R R/image_registration.R R/images.R R/interactivity.R R/interoperability.R R/python_environment.R R/python_hmrf.R R/python_scrublet.R R/spatial_enrichment.R R/spatial_genes.R R/spatial_in_situ_visuals.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 R/wnn.R R/zzz.R README.Rmd README.md

_pkgdown.yml

data/mini_giotto_3D.rda

data/mini_giotto_multi_cell.rda

data/mini_giotto_single_cell.rda

docs/.pkgdown.yml.BASE.16729.yml.swp

docs/.pkgdown.yml.BASE.6555.yml.swp

docs/.pkgdown.yml.LOCAL.16729.yml.swp

docs/.pkgdown.yml.REMOTE.16729.yml.swp

docs/.pkgdown.yml.swp

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docs/CODE_OF_CONDUCT.html

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docs/articles/Dimension_reduction.html

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docs/articles/Resolve_bc_210928.html

docs/articles/SeqFISH_cortex_210923.html

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docs/reference/removeCellAnnotation.html

docs/reference/removeFeatAnnotation.html

docs/reference/removeGiottoEnvironment.html

docs/reference/replaceGiottoInstructions.html

docs/reference/rescalePolygons.html

docs/reference/rescale_polygons.html

docs/reference/reshape_to_data_point.html

docs/reference/reshape_to_mesh_grid_obj.html

docs/reference/return_giotto_environment_path.html

docs/reference/return_giotto_environment_path_executable.html

docs/reference/rigid_transform_spatial_locations.html

docs/reference/rna_osmfish_normalization.html

docs/reference/rna_pears_resid_normalization.html

docs/reference/rna_standard_normalization.html

docs/reference/rotate_spatial_locations.html

docs/reference/row-plus-colnames-generic.html

docs/reference/rowMeans_flex.html

docs/reference/rowSums_flex.html

docs/reference/runDWLSDeconv.html

docs/reference/runFijiMacro.html

docs/reference/runGiottoHarmony.html

docs/reference/runHyperGeometricEnrich.html

docs/reference/runIntegratedUMAP.html

docs/reference/runPAGEEnrich.html

docs/reference/runPAGEEnrich_OLD.html

docs/reference/runPCA.html

docs/reference/runPCA_BiocSingular.html

docs/reference/runPCA_factominer.html

docs/reference/runPCA_prcomp_irlba.html

docs/reference/runPatternSimulation.html

docs/reference/runRankEnrich.html

docs/reference/runSpatialDeconv.html

docs/reference/runSpatialEnrich.html

docs/reference/runUMAP.html

docs/reference/runWNN.html

docs/reference/run_spat_autocor_global.html

docs/reference/run_spat_autocor_local.html

docs/reference/run_spatial_sim_tests_multi.html

docs/reference/run_spatial_sim_tests_one_rep.html

docs/reference/runtSNE.html

docs/reference/saveGiotto.html

docs/reference/scale_spatial_locations.html

docs/reference/screePlot.html

docs/reference/selectPatternGenes.html

docs/reference/select_gimage.html

docs/reference/setCellMetadata.html

docs/reference/setDimReduction.html

docs/reference/setExpression.html

docs/reference/setFeatureInfo.html

docs/reference/setFeatureMetadata.html

docs/reference/setGiottoImage.html

docs/reference/setMultiomics.html

docs/reference/setNearestNetwork.html

docs/reference/setPolygonInfo.html

docs/reference/setSpatialEnrichment.html

docs/reference/setSpatialGrid.html

docs/reference/setSpatialLocations.html

docs/reference/setSpatialNetwork.html

docs/reference/set_NearestNetwork.html

docs/reference/set_cell_id.html

docs/reference/set_cell_metadata.html

docs/reference/set_default_cow_n_col.html

docs/reference/set_default_feat_type.html

docs/reference/set_default_spat_unit.html

docs/reference/set_dimReduction.html

docs/reference/set_expression_values.html

docs/reference/set_feat_id.html

docs/reference/set_feature_info.html

docs/reference/set_giottoImage.html

docs/reference/set_giottoImage_MG.html

docs/reference/set_giottoLargeImage.html

docs/reference/set_giotto_python_path.html

docs/reference/set_multiomics.html

docs/reference/set_polygon_info.html

docs/reference/set_spatialGrid.html

docs/reference/set_spatialNetwork.html

docs/reference/set_spatial_enrichment.html

docs/reference/set_spatial_locations.html

docs/reference/seuratToGiotto.html

docs/reference/seuratToGiotto_OLD.html

docs/reference/shift_spatial_locations.html

docs/reference/shift_spatial_network.html

docs/reference/show-methods.html

docs/reference/showClusterDendrogram.html

docs/reference/showClusterHeatmap.html

docs/reference/showGiottoCellMetadata.html

docs/reference/showGiottoDimRed.html

docs/reference/showGiottoExpression.html

docs/reference/showGiottoFeatInfo.html

docs/reference/showGiottoFeatMetadata.html

docs/reference/showGiottoImageNames.html

docs/reference/showGiottoInstructions.html

docs/reference/showGiottoNearestNetworks.html

docs/reference/showGiottoSpatEnrichments.html

docs/reference/showGiottoSpatGrids.html

docs/reference/showGiottoSpatLocs.html

docs/reference/showGiottoSpatNetworks.html

docs/reference/showGiottoSpatialInfo.html

docs/reference/showGrids.html

docs/reference/showNetworks.html

docs/reference/showPattern.html

docs/reference/showPattern2D.html

docs/reference/showPattern3D.html

docs/reference/showPatternGenes.html

docs/reference/showProcessingSteps.html

docs/reference/showSaveParameters.html

docs/reference/showSpatialCorFeats.html

docs/reference/showSpatialCorGenes.html

docs/reference/signPCA.html

docs/reference/silhouetteRank.html

docs/reference/silhouetteRankTest.html

docs/reference/simulateOneGenePatternGiottoObject.html

docs/reference/slot.html

docs/reference/slotNames.html

docs/reference/smoothGiottoPolygons.html

docs/reference/solve_OLS_internal.html

docs/reference/solve_dampened_WLSj.html

docs/reference/sort_combine_two_DT_columns.html

docs/reference/spark.html

docs/reference/spatCellCellcom.html

docs/reference/spatCellCellcomSpots.html

docs/reference/spatCellPlot.html

docs/reference/spatCellPlot2D.html

docs/reference/spatData-class.html

docs/reference/spatDeconvPlot.html

docs/reference/spatDimCellPlot.html

docs/reference/spatDimCellPlot2D.html

docs/reference/spatDimFeatPlot2D.html

docs/reference/spatDimGenePlot.html

docs/reference/spatDimGenePlot2D.html

docs/reference/spatDimGenePlot3D.html

docs/reference/spatDimPlot.html

docs/reference/spatDimPlot2D.html

docs/reference/spatDimPlot3D.html

docs/reference/spatEnrObj-class.html

docs/reference/spatFeatData-class.html

docs/reference/spatFeatPlot2D.html

docs/reference/spatFeatPlot2D_single.html

docs/reference/spatGenePlot.html

docs/reference/spatGenePlot2D.html

docs/reference/spatGenePlot3D.html

docs/reference/spatIDs-generic.html

docs/reference/spatInSituPlotDensity.html

docs/reference/spatInSituPlotDensity_single.html

docs/reference/spatInSituPlotHex.html

docs/reference/spatInSituPlotHex_single.html

docs/reference/spatInSituPlotPoints.html

docs/reference/spatLocsObj-class.html

docs/reference/spatNetwDistributions.html

docs/reference/spatNetwDistributionsDistance.html

docs/reference/spatNetwDistributionsKneighbors.html

docs/reference/spatPlot.html

docs/reference/spatPlot2D.html

docs/reference/spatPlot2D_single.html

docs/reference/spatPlot3D.html

docs/reference/spatPlot_2D_plotly.html

docs/reference/spatPlot_3D_plotly.html

docs/reference/spatShift.html

docs/reference/spatUnit-generic.html

docs/reference/spatVector_to_dt.html

docs/reference/spatVector_to_dt2.html

docs/reference/spat_OR_func.html

docs/reference/spat_OR_func_DT.html

docs/reference/spat_fish_func.html

docs/reference/spat_fish_func_DT.html

docs/reference/spatialAEH.html

docs/reference/spatialAutoCor.html

docs/reference/spatialDE.html

docs/reference/spatialExperimentToGiotto.html

docs/reference/spatialGridObj-class.html

docs/reference/spatialNetworkObj-class.html

docs/reference/specificCellCellcommunicationScores.html

docs/reference/specific_CCCScores_spots.html

docs/reference/spin-generic.html

docs/reference/spline_poly.html

docs/reference/split_dendrogram_in_two.html

docs/reference/spot_deconvolution.html

docs/reference/standardise_flex.html

docs/reference/stitchFieldCoordinates.html

docs/reference/stitchGiottoLargeImage.html

docs/reference/stitchTileCoordinates.html

docs/reference/subClusterCells.html

docs/reference/subsetGiotto.html

docs/reference/subsetGiottoLocs.html

docs/reference/subsetGiottoLocsMulti.html

docs/reference/subsetGiottoLocsSubcellular.html

docs/reference/subset_cell_metadata.html

docs/reference/subset_feature_metadata.html

docs/reference/t_flex.html

docs/reference/time_format.html

docs/reference/trakem2_rigid_transf_extract.html

docs/reference/transform_2d_mesh_to_3d_mesh.html

docs/reference/transpose-generic.html

docs/reference/trendSceek.html

docs/reference/updateGiottoImage.html

docs/reference/updateGiottoImageMG.html

docs/reference/updateGiottoLargeImage.html

docs/reference/updateGiottoObject.html

docs/reference/updateGiottoPointsObject.html

docs/reference/updateGiottoPolygonObject.html

docs/reference/validObject.html

docs/reference/viewHMRFresults.html

docs/reference/viewHMRFresults2D.html

docs/reference/viewHMRFresults3D.html

docs/reference/violinPlot.html

docs/reference/wrap-generic.html

docs/reference/wrap_msg.html

docs/reference/wrap_txt.html

docs/reference/writeGiottoLargeImage.html

docs/reference/writeHMRFresults.html

docs/reference/write_giotto_viewer_annotation.html

docs/reference/write_giotto_viewer_dim_reduction.html

docs/reference/write_giotto_viewer_numeric_annotation.html

docs/reference/xy_translate_spatial_locations.html

docs/sitemap.xml

index.Rmd index.md

inst/CITATION

inst/extdata/additional_r_packages.txt

inst/extdata/datasets.txt

inst/extdata/giotto_python_modules.txt

inst/extdata/mouse_ligand_receptors.txt

inst/extdata/sig_matrix.txt

inst/fiji/Headless_RVSS.py

inst/images/MerFISH_hypoth/210924_results/0-filterDistributions.png

inst/images/MerFISH_hypoth/210924_results/1-filterDistributions.png

inst/images/MerFISH_hypoth/210924_results/10-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210924_results/11-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210924_results/12-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210924_results/13-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210924_results/14-UMAP_3D.png

inst/images/MerFISH_hypoth/210924_results/15-spat3D.png

inst/images/MerFISH_hypoth/210924_results/16-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/17-spat3D.png

inst/images/MerFISH_hypoth/210924_results/18-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/19-spat3D.png

inst/images/MerFISH_hypoth/210924_results/2-filterCombinations.png

inst/images/MerFISH_hypoth/210924_results/20-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/21-spat3D.png

inst/images/MerFISH_hypoth/210924_results/22-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/23-spat3D.png

inst/images/MerFISH_hypoth/210924_results/24-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/3-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/4-spat3D.png

inst/images/MerFISH_hypoth/210924_results/5-screePlot.png

inst/images/MerFISH_hypoth/210924_results/6-UMAP_3D.png

inst/images/MerFISH_hypoth/210924_results/7-UMAP_3D.png

inst/images/MerFISH_hypoth/210924_results/8-spatPlot2D.png

inst/images/MerFISH_hypoth/210924_results/9-violinPlot.png

inst/images/MerFISH_hypoth/210927_results/0-filterDistributions.png

inst/images/MerFISH_hypoth/210927_results/1-filterDistributions.png

inst/images/MerFISH_hypoth/210927_results/10-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210927_results/11-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210927_results/12-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210927_results/13-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/210927_results/14-UMAP3D.png

inst/images/MerFISH_hypoth/210927_results/15-spatplot3D.png

inst/images/MerFISH_hypoth/210927_results/16-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/18-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/2-filterCombinations.png

inst/images/MerFISH_hypoth/210927_results/20-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/22-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/23-spatplot3D.png

inst/images/MerFISH_hypoth/210927_results/24-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/25-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/26-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/27-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/3-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/5-screePlot.png

inst/images/MerFISH_hypoth/210927_results/8-spatPlot2D.png

inst/images/MerFISH_hypoth/210927_results/9-violinPlot.png

inst/images/MerFISH_hypoth/211001_results/0-filterDistributions.png

inst/images/MerFISH_hypoth/211001_results/1-filterDistributions.png

inst/images/MerFISH_hypoth/211001_results/10-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/11-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/12-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/13-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/14-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/15-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/16-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/17-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/18-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/19-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/211001_results/2-filterCombinations.png

inst/images/MerFISH_hypoth/211001_results/20-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/211001_results/21-UMAP_2D.png

inst/images/MerFISH_hypoth/211001_results/22-showClusterHeatmap.png

inst/images/MerFISH_hypoth/211001_results/3-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/4-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/5-showClusterHeatmap.png

inst/images/MerFISH_hypoth/211001_results/6-showClusterDendrogram.png

inst/images/MerFISH_hypoth/211001_results/7-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/8-spatPlot2D.png

inst/images/MerFISH_hypoth/211001_results/9-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/0-filterDistributions.png

inst/images/MerFISH_hypoth/220915_results/1-filterDistributions.png

inst/images/MerFISH_hypoth/220915_results/10-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/220915_results/11-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/220915_results/12-plotMetaDataHeatmap.png

inst/images/MerFISH_hypoth/220915_results/13-UMAP_3D.png

inst/images/MerFISH_hypoth/220915_results/14-spat3D.png

inst/images/MerFISH_hypoth/220915_results/15-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/16-spat3D.png

inst/images/MerFISH_hypoth/220915_results/17-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/18-spat3D.png

inst/images/MerFISH_hypoth/220915_results/19-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/2-filterCombinations.png

inst/images/MerFISH_hypoth/220915_results/20-spat3D.png

inst/images/MerFISH_hypoth/220915_results/21-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/22-spat3D.png

inst/images/MerFISH_hypoth/220915_results/23-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/3-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/4-spat3D.png

inst/images/MerFISH_hypoth/220915_results/5-screePlot.png

inst/images/MerFISH_hypoth/220915_results/6-UMAP_3D.png

inst/images/MerFISH_hypoth/220915_results/7-UMAP_3D.png

inst/images/MerFISH_hypoth/220915_results/8-spatPlot2D.png

inst/images/MerFISH_hypoth/220915_results/9-violinPlot.png

inst/images/Resolve_bc/210928/0-spatPlot2D.png

inst/images/Resolve_bc/210928/1-spatPlot2D.png

inst/images/Resolve_bc/210928/10-spatDimPlot2D.png

inst/images/Resolve_bc/210928/12-showClusterDendrogram.png

inst/images/Resolve_bc/210928/13-spatPlot2D.png

inst/images/Resolve_bc/210928/14-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/15-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/16-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/17-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/18-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/19-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/2-spatPlot2D.png

inst/images/Resolve_bc/210928/20-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/21-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/22-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/23-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/24-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/25-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/26-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/27-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/28-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/29-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/3-spatPlot2D.png

inst/images/Resolve_bc/210928/30-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/31-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/32-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/33-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/34-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/35-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/36-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/37-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/38-UMAP.png

inst/images/Resolve_bc/210928/39-UMAP.png

inst/images/Resolve_bc/210928/4-HVFplot.png

inst/images/Resolve_bc/210928/40-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/41-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/42-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/43-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/44-spatPlot2D.png

inst/images/Resolve_bc/210928/46-spatPlot2D.png

inst/images/Resolve_bc/210928/47-spatPlot2D.png

inst/images/Resolve_bc/210928/48-spatPlot2D.png

inst/images/Resolve_bc/210928/49-screePlot.png

inst/images/Resolve_bc/210928/5-HVFplot.png

inst/images/Resolve_bc/210928/50-spatDimPlot2D.png

inst/images/Resolve_bc/210928/51-spatDimPlot2D.png

inst/images/Resolve_bc/210928/52-spatPlot2D.png

inst/images/Resolve_bc/210928/53-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/54-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/55-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/56-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/57-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/58-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/59-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/6-screePlot.png

inst/images/Resolve_bc/210928/60-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/61-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/62-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/63-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/64-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/65-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/66-spatInSituPlotPoints.png

inst/images/Resolve_bc/210928/69-spatPlot2D.png

inst/images/Resolve_bc/210928/7-PCA.png

inst/images/Resolve_bc/210928/71-showClusterHeatmap.png

inst/images/Resolve_bc/210928/72-Heatmap.png

inst/images/Resolve_bc/210928/8-UMAP.png

inst/images/Resolve_bc/210928/9-UMAP.png

inst/images/SeqFish_mouse_cortex/0-HVFplot.png

inst/images/SeqFish_mouse_cortex/0-filterDistributions.png

inst/images/SeqFish_mouse_cortex/0-spatPlot2D.png

inst/images/SeqFish_mouse_cortex/1-HVFplot.png

inst/images/SeqFish_mouse_cortex/1-filterDistributions.png

inst/images/SeqFish_mouse_cortex/10-UMAP.png

inst/images/SeqFish_mouse_cortex/10-filterDistributions.png

inst/images/SeqFish_mouse_cortex/11-filterCombinations.png

inst/images/SeqFish_mouse_cortex/11-showClusterHeatmap.pdf

inst/images/SeqFish_mouse_cortex/11-showClusterHeatmap.png

inst/images/SeqFish_mouse_cortex/12-filterCombinations.png

inst/images/SeqFish_mouse_cortex/12-showClusterDendrogram.png

inst/images/SeqFish_mouse_cortex/12_d_network_cell_cell_enrichment_self.png

inst/images/SeqFish_mouse_cortex/13-spatDimPlot2D.png

inst/images/SeqFish_mouse_cortex/14-spatDimPlot2D.png

inst/images/SeqFish_mouse_cortex/15-violinPlot.png

inst/images/SeqFish_mouse_cortex/16-plotMetaDataHeatmap.png

inst/images/SeqFish_mouse_cortex/17-violinPlot.png

inst/images/SeqFish_mouse_cortex/18-spatDimPlot2D.png

inst/images/SeqFish_mouse_cortex/19-plotHeatmap.png

inst/images/SeqFish_mouse_cortex/2-HVFplot.png

inst/images/SeqFish_mouse_cortex/2-filterCombinations.png

inst/images/SeqFish_mouse_cortex/2-screePlot.png

inst/images/SeqFish_mouse_cortex/20-plotHeatmap.png

inst/images/SeqFish_mouse_cortex/21-spatPlot2D.png

inst/images/SeqFish_mouse_cortex/22-spatPlot2D.png

inst/images/SeqFish_mouse_cortex/23-spatPlot2D.png

inst/images/SeqFish_mouse_cortex/24-spatPlot2D.png

inst/images/SeqFish_mouse_cortex/25-spatPlot2D.png

inst/images/SeqFish_mouse_cortex/26-spatGenePlot2D.png

inst/images/SeqFish_mouse_cortex/27-heatmSpatialCorFeats.pdf

inst/images/SeqFish_mouse_cortex/27-heatmSpatialCorFeats.png

inst/images/SeqFish_mouse_cortex/28-rankSpatialCorGroups.png

inst/images/SeqFish_mouse_cortex/29-spatCellPlot2D.png

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inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/annotation_num_list_rna.txt

inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/centroid_locations.txt

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inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/giotto_rna_ids.txt

inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/offset_file.txt

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inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/rna_HMRF_2_k9_b.28_annot_information.txt

inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/rna_cell_types_annot_information.annot

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inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/rna_leiden_clus_annot_information.annot

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inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/rna_total_expr_num_annot_information.txt

inst/images/images/images/SeqFish_mouse_cortex/Mouse_cortex_viewer/umap_umap_dim_coord.txt

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inst/python/SpatialDE_wrapper.py

inst/python/ad2g.py

inst/python/configuration/genv_current.yml

inst/python/configuration/genv_old_stable.yml

inst/python/g2ad.py

inst/python/get_result2.py

inst/python/python_leiden.py

inst/python/python_louvain.py

inst/python/python_scrublet.py

inst/python/python_segmentation.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

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tests/testthat.R tests/testthat/test_accessors.R tests/testthat/test_createObject.R tests/testthat/test_dataImports.R tests/testthat/test_giottoEnv.R tests/testthat/test_giottoInstr.R tests/testthat/test_gobject.R tests/testthat/test_merFISH.R

vignettes/.gitignore

vignettes/Dimension_reduction.Rmd vignettes/Installation_issues_python_env.Rmd vignettes/Nanostring_Lung12_jan26_21.Rmd vignettes/Resolve_bc_210928.Rmd vignettes/SeqFISH_cortex_210923.Rmd vignettes/Visium_prostate_integration_Sep30_21.Rmd vignettes/Visualizations.Rmd vignettes/analyses_deconvolution_Oct2021.Rmd vignettes/configuration.Rmd vignettes/contribute.Rmd vignettes/data_processing.Rmd vignettes/datasets_overview.Rmd vignettes/faqs.Rmd vignettes/getting_started.Rmd vignettes/getting_started_gobject.Rmd vignettes/getting_started_images.Rmd vignettes/getting_started_instructions.Rmd vignettes/getting_started_saving.Rmd vignettes/giotto_news.Rmd vignettes/github_issues.Rmd vignettes/installation_issues.Rmd vignettes/merFISH_hypoth_210924.Rmd vignettes/merFISH_hypoth_220915.Rmd vignettes/mini_seqfish.Rmd vignettes/mini_starmap.Rmd vignettes/mini_visium.Rmd vignettes/mouse_codex_spleen_Sep29_21.Rmd vignettes/mouse_visium_brain_220328.Rmd vignettes/mouse_visium_brain_220426.Rmd vignettes/mouse_visium_brain_Sep30_21.Rmd vignettes/mouse_visium_kidney_210830.Rmd vignettes/nanostring_examples_overview.Rmd vignettes/osmFISH_mouse_SScortex_Sep29_21.Rmd vignettes/overview/giotto_input.Rmd vignettes/overview/temp_construction.Rmd vignettes/singlecell_prostate_integration_Sep30_21.Rmd vignettes/singlecell_prostate_standard_Sep29_21.Rmd vignettes/temp_construction.Rmd vignettes/vizgen_mouse_brain_210929.Rmd

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