adapt_aspect_ratio | adapt_aspect_ratio |
addCellIntMetadata | addCellIntMetadata |
addCellMetadata | addCellMetadata |
addCellStatistics | addCellStatistics |
addGeneMetadata | addGeneMetadata |
addGenesPerc | addGenesPerc |
addGeneStatistics | addGeneStatistics |
addGiottoImage | addGiottoImage |
addGiottoImageToSpatPlot | addGiottoImageToSpatPlot |
addHMRF | addHMRF |
addHMRF_V2 | addHMRF_V2 |
addNetworkLayout | addNetworkLayout |
addStatistics | addStatistics |
adjustGiottoMatrix | adjustGiottoMatrix |
aes_string2 | aes_string2 |
all_plots_save_function | all_plots_save_function |
anndataToGiotto | anndataToGiotto |
annotateGiotto | annotateGiotto |
annotateSpatialGrid | annotateSpatialGrid |
annotateSpatialNetwork | annotateSpatialNetwork |
annotate_spatlocs_with_spatgrid_2D | annotate_spatlocs_with_spatgrid_2D |
annotate_spatlocs_with_spatgrid_3D | annotate_spatlocs_with_spatgrid_3D |
average_gene_gene_expression_in_groups | average_gene_gene_expression_in_groups |
binSpect | binSpect |
binSpectMulti | binSpectMulti |
binSpectSingle | binSpectSingle |
calc_spatial_enrichment_DT | calc_spatial_enrichment_DT |
calc_spatial_enrichment_matrix | calc_spatial_enrichment_matrix |
calc_spatial_enrichment_minimum | calc_spatial_enrichment_minimum |
calculate_distance_and_weight | calculate_distance_and_weight |
calculateHVG | calculateHVG |
calculateMetaTable | calculateMetaTable |
calculateMetaTableCells | calculateMetaTableCells |
cal_diff_per_interaction | cal_diff_per_interaction |
cal_expr_residual | cal_expr_residual |
cellProximityBarplot | cellProximityBarplot |
cellProximityEnrichment | cellProximityEnrichment |
cellProximityEnrichmentEachSpot | cellProximityEnrichmentEachSpot |
cellProximityEnrichmentSpots | cellProximityEnrichmentSpots |
cellProximityHeatmap | cellProximityHeatmap |
cellProximityNetwork | cellProximityNetwork |
cellProximitySpatPlot | cellProximitySpatPlot |
cellProximitySpatPlot2D | cellProximitySpatPlot2D |
cellProximitySpatPlot3D | cellProximitySpatPlot2D |
cell_proximity_spots | cell_proximity_spots |
cell_proximity_spots_external | cell_proximity_spots_external |
cell_proximity_spots_internal | cell_proximity_spots_internal |
cellProximityVisPlot | cellProximityVisPlot |
cellProximityVisPlot_2D_ggplot | cellProximityVisPlot_2D_ggplot |
cellProximityVisPlot_2D_plotly | cellProximityVisPlot_2D_plotly |
cellProximityVisPlot_3D_plotly | cellProximityVisPlot_3D_plotly |
changeGiottoInstructions | changeGiottoInstructions |
changeImageBg | changeImageBg |
checkAndFixSpatialGenes | checkAndFixSpatialGenes |
checkGiottoEnvironment | checkGiottoEnvironment |
chooseAvailableSpatialGenes | chooseAvailableSpatialGenes |
clusterCells | clusterCells |
cluster_enrich_analysis | cluster_enrich_analysis |
clusterSpatialCorGenes | clusterSpatialCorGenes |
colMeans_flex | colMeans_flex |
colMeans_giotto | colMeans_giotto |
colSums_flex | colSums_flex |
colSums_giotto | colSums_giotto |
combCCcom | combCCcom |
combineCellProximityGenes | combineCellProximityGenes |
combineCellProximityGenes_per_interaction | combineCellProximityGenes_per_interaction |
combineCPG | combineCPG |
combineICG | combineICG |
combineInteractionChangedGenes | combineInteractionChangedGenes |
combineMetadata | combineMetadata |
convertEnsemblToGeneSymbol | convertEnsemblToGeneSymbol |
convert_mgImage_to_array_DT | convert_mgImage_to_array_DT |
convert_to_full_spatial_network | convert_to_full_spatial_network |
convert_to_reduced_spatial_network | convert_to_reduced_spatial_network |
cor_flex | cor_flex |
cor_giotto | cor_giotto |
cor_sparse | cor_sparse adapted from wydr package |
create_2d_mesh_grid_line_obj | create_2d_mesh_grid_line_obj |
create_average_detection_DT | create_average_detection_DT |
create_average_DT | create_average_DT |
create_cell_type_random_cell_IDs | create_cell_type_random_cell_IDs |
create_cluster_matrix | create_cluster_matrix |
createCrossSection | createCrossSection |
create_crossSection_object | create_crossSection_object |
create_delaunayNetwork2D | create_delaunayNetwork2D |
create_delaunayNetwork3D | create_delaunayNetwork3D |
create_delaunayNetwork_deldir | create_delaunayNetwork_deldir |
create_delaunayNetwork_geometry | create_delaunayNetwork_geometry |
create_delaunayNetwork_geometry_3D | create_delaunayNetwork_geometry_3D |
create_delaunayNetwork_RTriangle | create_delaunayNetwork_RTriangle |
create_dimObject | create_dimObject |
create_genes_to_use_matrix | create_genes_to_use_matrix |
createGiottoImage | createGiottoImage |
createGiottoInstructions | createGiottoInstructions |
createGiottoObject | create Giotto object |
createGiottoVisiumObject | createGiottoVisiumObject |
createHeatmap_DT | createHeatmap_DT |
create_jackstrawplot | create_jackstrawplot |
create_KNNnetwork_dbscan | create_KNNnetwork_dbscan |
create_mesh_grid_lines | create_mesh_grid_lines |
createMetagenes | createMetagenes |
createNearestNetwork | createNearestNetwork |
createRegZStackGobject | createRegZStackGobject |
create_screeplot | create_screeplot |
createSpatialDefaultGrid | createSpatialDefaultGrid |
createSpatialDelaunayNetwork | createSpatialDelaunayNetwork |
createSpatialEnrich | createSpatialEnrich |
createSpatialGrid | createSpatialGrid |
create_spatialGrid_default_2D | create_spatialGrid_default_2D |
create_spatialGrid_default_3D | create_spatialGrid_default_3D |
create_spatialGridObject | create_spatialGridObject |
createSpatialKNNnetwork | createSpatialKNNnetwork |
createSpatialNetwork | createSpatialNetwork |
create_spatialNetworkObject | create_spatialNetworkObject |
crossSectionGenePlot | crossSectionGenePlot |
crossSectionGenePlot3D | crossSectionGenePlot3D |
crossSectionPlot | crossSectionPlot |
crossSectionPlot3D | crossSectionPlot3D |
decide_cluster_order | decide_cluster_order |
detectSpatialCorGenes | detectSpatialCorGenes |
detectSpatialPatterns | detectSpatialPatterns |
determine_cores | determine_cores |
dimCellPlot | dimCellPlot |
dimCellPlot2D | dimCellPlot2D |
dimGenePlot | dimGenePlot |
dimGenePlot2D | dimGenePlot2D |
dimGenePlot3D | dimGenePlot3D |
dimPlot | dimPlot |
dimPlot2D | dimPlot2D |
dimPlot_2D_plotly | dimPlot_2D_plotly |
dimPlot2D_single | dimPlot2D_single |
dimPlot3D | dimPlot3D |
dimPlot_3D_plotly | dimPlot_3D_plotly |
do_cell_proximity_test | do_cell_proximity_test |
do_cell_proximity_test_spot | do_cell_proximity_test_spot |
doHclust | doHclust |
doHMRF | doHMRF |
doHMRF_V2 | doHMRF_V2 |
doKmeans | doKmeans |
doLeidenCluster | doLeidenCluster |
doLeidenSubCluster | doLeidenSubCluster |
do_limmatest | do_limmatest |
doLouvainCluster | doLouvainCluster |
doLouvainCluster_community | doLouvainCluster_community |
doLouvainCluster_multinet | doLouvainCluster_multinet |
doLouvainSubCluster | doLouvainSubCluster |
doLouvainSubCluster_community | doLouvainSubCluster_community |
doLouvainSubCluster_multinet | doLouvainSubCluster_multinet |
do_multi_permuttest_random | do_multi_permuttest_random |
do_multi_permuttest_random_spot | do_multi_permuttest_random_spot |
do_page_permutation | do_page_permutation |
do_permuttest_original | do_permuttest_original |
do_permuttest_original_spot | do_permuttest_original_spot |
do_permuttest_random | do_permuttest_random |
do_permuttest_random_spot | do_permuttest_random_spot |
do_permuttest_spot | do_permuttest_spot |
doRandomWalkCluster | doRandomWalkCluster |
do_rank_permutation | do_rank_permutation |
doSNNCluster | doSNNCluster |
do_spatial_grid_averaging | do_spatial_grid_averaging |
do_spatial_knn_smoothing | do_spatial_knn_smoothing |
do_ttest | do_ttest |
do_wilctest | do_wilctest |
DT_removeNA | DT_removeNA |
dt_to_matrix | dt_to_matrix |
enrich_analysis | enrich_analysis |
enrich_deconvolution | enrich_deconvolution |
estimateCellCellDistance | estimateCellCellDistance |
estimateImageBg | estimateImageBg |
evaluate_expr_matrix | evaluate_expr_matrix |
evaluate_spatial_locations | evaluate_spatial_locations |
explainGiottoInstructions | explainGiottoInstructions |
exportGiottoViewer | exportGiottoViewer |
exprCellCellcom | exprCellCellcom |
extended_gini_fun | extended_gini_fun |
extend_vector | extend_vector |
extractNearestNetwork | extractNearestNetwork |
fDataDT | fDataDT |
filterCellProximityGenes | filterCellProximityGenes |
filterCombinations | filterCombinations |
filterCPG | filterCPG |
filterDistributions | filterDistributions |
filterGiotto | filterGiotto |
filterICG | filterICG |
filterICGSpot | filterICGSpot |
filterInteractionChangedGenes | filterInteractionChangedGenes |
filter_network | filter_network |
filterSpatialGenes | filterSpatialGenes |
findCellProximityGenes | findCellProximityGenes |
findCellProximityGenes_per_interaction | findCellProximityGenes_per_interaction |
findCPG | findCPG |
find_dampening_constant | find_dampening_constant |
findGiniMarkers | findGiniMarkers |
findGiniMarkers_one_vs_all | findGiniMarkers_one_vs_all |
find_grid_2D | find_grid_2D |
find_grid_3D | find_grid_3D |
find_grid_x | find_grid_x |
find_grid_y | find_grid_y |
find_grid_z | find_grid_z |
findICG | findICG |
findICG_per_interaction_spot | findICG_per_interaction_spot |
findICGSpot | findICGSpot |
findInteractionChangedGenes | findInteractionChangedGenes |
findMarkers | findMarkers |
findMarkers_one_vs_all | findMarkers_one_vs_all |
findMastMarkers | findMastMarkers |
findMastMarkers_one_vs_all | findMastMarkers_one_vs_all |
findNetworkNeighbors | findNetworkNeighbors |
findScranMarkers | findScranMarkers |
findScranMarkers_one_vs_all | findScranMarkers_one_vs_all |
find_x_y_ranges | find_x_y_ranges |
flex_lapply | flex_lapply |
FSV_show | FSV_show |
geneExpDWLS | geneExpDWLS |
general_save_function | general_save_function |
get10Xmatrix | get10Xmatrix |
get10Xmatrix_h5 | get10Xmatrix_h5 |
getClusterSimilarity | getClusterSimilarity |
get_cross_section_coordinates | get_cross_section_coordinates |
getDendrogramSplits | getDendrogramSplits |
get_distance | get_distance |
getDistinctColors | getDistinctColors |
getGiottoImage | getGiottoImage |
get_os | get_os |
get_sectionThickness | get_sectionThickness |
getSpatialDataset | getSpatialDataset |
ggplot_save_function | ggplot_save_function |
giotto-class | S4 giotto Class |
giotto_lapply | giotto_lapply |
heatmSpatialCorGenes | heatmSpatialCorGenes |
hyperGeometricEnrich | hyperGeometricEnrich |
initHMRF_V2 | initHMRF_V2 |
insertCrossSectionGenePlot3D | insertCrossSectionGenePlot3D |
insertCrossSectionSpatPlot3D | insertCrossSectionSpatPlot3D |
install_giotto_environment | install_giotto_environment |
installGiottoEnvironment | installGiottoEnvironment |
install_giotto_environment_specific | install_giotto_environment_specific |
jackstrawPlot | jackstrawPlot |
join_expression | join_expression |
kmeans_arma_binarize | kmeans_arma_binarize |
kmeans_arma_subset_binarize | kmeans_arma_subset_binarize |
kmeans_binarize | kmeans_binarize |
kmeans_binarize_wrapper | kmeans_binarize_wrapper |
lapply_flex | lapply_flex |
libNorm_giotto | libNorm_giotto |
loadHMRF | loadHMRF |
logNorm_giotto | logNorm_giotto |
makeSignMatrixDWLS | makeSignMatrixDWLS |
makeSignMatrixDWLSfromMatrix | makeSignMatrixDWLSfromMatrix |
makeSignMatrixPAGE | makeSignMatrixPAGE |
makeSignMatrixRank | makeSignMatrixRank |
make_simulated_network | make_simulated_network |
mean_expr_det_test | mean_expr_det_test |
mean_flex | mean_flex |
mean_giotto | mean_giotto |
mergeClusters | mergeClusters |
mini_giotto_3D | mini Giotto object for spatial single-cell 3D data |
mini_giotto_multi_cell | mini Giotto object for spatial multi-cell resolution data |
mini_giotto_single_cell | mini Giotto object for spatial single-cell resolution data |
my_arowMeans | my_arowMeans |
mygini_fun | mygini_fun |
my_growMeans | my_growMeans |
my_rowMeans | my_rowMeans |
nnDT_to_kNN | nnDT_to_kNN |
node_clusters | node_clusters |
normalizeGiotto | normalizeGiotto |
numPts_below_line | numPts_below_line |
optimize_deconvolute_dwls | optimize_deconvolute_dwls |
optimize_solveDampenedWLS | optimize_solveDampenedWLS |
OR_test_fnc | OR_test_fnc |
package_check | package_check |
PAGE_DT_method | PAGE_DT_method |
PAGEEnrich | PAGEEnrich |
pca_giotto | pca_giotto |
pDataDT | pDataDT |
pipe | Pipe operator |
plotCCcomDotplot | plotCCcomDotplot |
plotCCcomHeatmap | plotCCcomHeatmap |
plotCellProximityGenes | plotCellProximityGenes |
plotCellProximityGenesSpot | plotCellProximityGenesSpot |
plotCombineCCcom | plotCombineCCcom |
plotCombineCellCellCommunication | plotCombineCellCellCommunication |
plotCombineCellProximityGenes | plotCombineCellProximityGenes |
plotCombineCPG | plotCombineCPG |
plotCombineICG | plotCombineICG |
plotCombineInteractionChangedGenes | plotCombineInteractionChangedGenes |
plotCPG | plotCPG |
plotGiottoImage | plotGiottoImage |
plotHeatmap | plotHeatmap |
plotICG | plotICG |
plotICGSpot | plotICGSpot |
plotInteractionChangedGenes | plotInteractionChangedGenes |
plotly_axis_scale_2D | plotly_axis_scale_2D |
plotly_axis_scale_3D | plotly_axis_scale_3D |
plotly_grid | plotly_grid |
plotly_network | plotly_network |
plotMetaDataCellsHeatmap | plotMetaDataCellsHeatmap |
plotMetaDataHeatmap | plotMetaDataHeatmap |
plot_network_layer_ggplot | plot_network_layer_ggplot |
plotPCA | plotPCA |
plotPCA_2D | plotPCA_2D |
plotPCA_3D | plotPCA_3D |
plot_point_layer_ggplot | plot_point_layer_ggplot |
plot_point_layer_ggplot_noFILL | plot_point_layer_ggplot_noFILL |
plotRankSpatvsExpr | plotRankSpatvsExpr |
plotRecovery | plotRecovery |
plotRecovery_sub | plotRecovery_sub |
plot_spat_image_layer_ggplot | plot_spat_image_layer_ggplot |
plot_spat_point_layer_ggplot | plot_spat_point_layer_ggplot |
plot_spat_point_layer_ggplot_noFILL | plot_spat_point_layer_ggplot_noFILL |
plot_spat_scatterpie_layer_ggplot | plot_spat_scatterpie_layer_ggplot |
plot_spat_voronoi_layer_ggplot | plot_spat_voronoi_layer_ggplot |
plotStatDelaunayNetwork | plotStatDelaunayNetwork |
plotTSNE | plotTSNE |
plotTSNE_2D | plotTSNE_2D |
plotTSNE_3D | plotTSNE_3D |
plotUMAP | plotUMAP |
plotUMAP_2D | plotUMAP_2D |
plotUMAP_3D | plotUMAP_3D |
processGiotto | processGiotto |
projection_fun | projection_fun |
rank_binarize | rank_binarize |
rankEnrich | rankEnrich |
rankSpatialCorGroups | rankSpatialCorGroups |
read_crossSection | read_crossSection |
readExprMatrix | readExprMatrix |
readGiottoInstructions | readGiottoInstrunctions |
register_spatial_locations | register_spatial_locations |
removeCellAnnotation | removeCellAnnotation |
removeGeneAnnotation | removeGeneAnnotation |
removeGiottoEnvironment | removeGiottoEnvironment |
replaceGiottoInstructions | replaceGiottoInstructions |
reshape_to_data_point | reshape_to_data_point |
reshape_to_mesh_grid_obj | reshape_to_mesh_grid_obj |
return_giotto_environment_path | return_giotto_environment_path |
return_giotto_environment_path_executable | return_giotto_environment_path_executable |
rotate_spatial_locations | rotate_spatial_locations |
rowMeans_flex | rowMeans_flex |
rowMeans_giotto | rowMeans_giotto |
rowSums_flex | rowSums_flex |
rowSums_giotto | rowSums_giotto |
runDWLSDeconv | runDWLSDeconv |
runHyperGeometricEnrich | runHyperGeometricEnrich |
runPAGEEnrich | runPAGEEnrich |
runPAGEEnrich_OLD | runPAGEEnrich_OLD |
runPatternSimulation | runPatternSimulation |
runPCA | runPCA |
runPCA_factominer | runPCA_factominer |
runPCA_prcomp_irlba | runPCA_prcomp_irlba |
runRankEnrich | runRankEnrich |
runSpatialDeconv | runSpatialDeconv |
runSpatialEnrich | runSpatialEnrich |
run_spatial_sim_tests_multi | run_spatial_sim_tests_multi |
run_spatial_sim_tests_one_rep | run_spatial_sim_tests_one_rep |
runtSNE | runtSNE |
runUMAP | runUMAP |
sampling_sp_genes | sampling_sp_genes |
scale_spatial_locations | scale_spatial_locations |
screePlot | screePlot |
select_dimReduction | select_dimReduction |
select_expression_values | select_expression_values |
select_NearestNetwork | select_NearestNetwork |
selectPatternGenes | selectPatternGenes |
select_spatialGrid | select_spatialGrid |
select_spatialNetwork | select_spatialNetwork |
set_giotto_python_path | set_giotto_python_path |
showClusterDendrogram | showClusterDendrogram |
showClusterHeatmap | showClusterHeatmap |
showGiottoImageNames | showGiottoImageNames |
showGiottoInstructions | showGiottoInstructions |
showGrids | showGrids |
show-methods | show method for giotto class |
showNetworks | showNetworks |
showPattern | showPattern |
showPattern2D | showPattern2D |
showPattern3D | showPattern3D |
showPatternGenes | showPatternGenes |
showProcessingSteps | showProcessingSteps |
showSaveParameters | showSaveParameters |
showSpatialCorGenes | showSpatialCorGenes |
signPCA | signPCA |
silhouetteRank | silhouetteRank |
silhouetteRankTest | silhouetteRankTest |
simulateOneGenePatternGiottoObject | simulateOneGenePatternGiottoObject |
solve_dampened_WLSj | solve_dampened_WLSj |
solve_OLS_internal | solve_OLS_internal |
sort_combine_two_DT_columns | sort_combine_two_DT_columns |
spark | spark |
spatCellCellcom | spatCellCellcom |
spatCellCellcomSpots | spatCellCellcomSpots |
spatCellPlot | spatCellPlot |
spatCellPlot2D | spatCellPlot2D |
spatDeconvPlot | spatDeconvPlot |
spatDimCellPlot | spatDimCellPlot |
spatDimCellPlot2D | spatDimCellPlot2D |
spatDimGenePlot | spatDimGenePlot |
spatDimGenePlot2D | spatDimGenePlot2D |
spatDimGenePlot3D | spatDimGenePlot3D |
spatDimPlot | spatDimPlot |
spatDimPlot2D | spatDimPlot2D |
spatDimPlot3D | spatDimPlot3D |
spat_fish_func | spat_fish_func |
spat_fish_func_DT | spat_fish_func_DT |
spatGenePlot | spatGenePlot |
spatGenePlot2D | spatGenePlot2D |
spatGenePlot3D | spatGenePlot3D |
spatialAEH | spatialAEH |
spatialDE | spatialDE |
spatNetwDistributions | spatNetwDistributionsDistance |
spatNetwDistributionsDistance | spatNetwDistributionsDistance |
spatNetwDistributionsKneighbors | spatNetwDistributionsKneighbors |
spat_OR_func | spat_OR_func |
spat_OR_func_DT | spat_OR_func_DT |
spatPlot | spatPlot |
spatPlot2D | spatPlot2D |
spatPlot_2D_plotly | spatPlot_2D_plotly |
spatPlot2D_single | spatPlot2D_single |
spatPlot3D | spatPlot3D |
spatPlot_3D_plotly | spatPlot_3D_plotly |
specific_CCCScores_spots | specific_CCCScores_spots |
specificCellCellcommunicationScores | specificCellCellcommunicationScores |
split_dendrogram_in_two | split_dendrogram_in_two |
spot_deconvolution | spot_deconvolution |
stack_spatlocs | stack_spatlocs |
standardise_flex | standardise_flex |
standardise_giotto | standardise_giotto |
stitchFieldCoordinates | stitchFieldCoordinates |
stitchTileCoordinates | stitchTileCoordinates |
subClusterCells | subClusterCells |
subsetGiotto | subsetGiotto |
subsetGiottoLocs | subsetGiottoLocs |
t_flex | t_flex |
t_giotto | t_giotto |
trakem2_rigid_transf_extract | trakem2_rigid_transf_extract |
transform_2d_mesh_to_3d_mesh | transform_2d_mesh_to_3d_mesh |
trendSceek | trendSceek |
updateGiottoImage | updateGiottoImage |
viewHMRFresults | viewHMRFresults |
viewHMRFresults2D | viewHMRFresults2D |
viewHMRFresults3D | viewHMRFresults3D |
viewHMRFresults_V2 | viewHMRFresults_V2 |
violinPlot | violinPlot |
write_giotto_viewer_annotation | write_giotto_viewer_annotation |
write_giotto_viewer_dim_reduction | write_giotto_viewer_dim_reduction |
write_giotto_viewer_numeric_annotation | write_giotto_viewer_numeric_annotation |
writeHMRFresults | writeHMRFresults |
xy_translate_spatial_locations | xy_translate_spatial_locations |
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