API for RubD/Giotto
Spatial single-cell transcriptomics pipeline.

Global functions
%>% Man page
FSV_show Man page
FUN Source code
GenePattern_show Man page
OR_function2 Man page Source code
Spatial_AEH Man page
Spatial_DE Man page
addCellMetadata Man page
addCellStatistics Man page
addGeneMetadata Man page
addGeneStatistics Man page
addHMRF Man page
addNetworkLayout Man page
addStatistics Man page
adjustGiottoMatrix Man page
allCellCellcommunicationsScores Man page
all_plots_save_function Man page Source code
annotateGiotto Man page
annotateSpatialNetwork Man page Source code
annotate_spatlocs_with_spatgrid_2D Man page
annotate_spatlocs_with_spatgrid_3D Man page
average_gene_gene_expression_in_groups Man page
binGetSpatialGenes Man page Source code
calculateHVG Man page Source code
calculateMetaTable Man page
calculateSpatialGenes Man page
calculate_spatial_genes_python Man page
cellProximityBarplot Man page Source code
cellProximityEnrichment Man page
cellProximityHeatmap Man page Source code
cellProximityNetwork Man page Source code
cellProximitySpatPlot2D Man page
cellProximityVisPlot Man page
cellProximityVisPlot_2D_ggplot Man page
cellProximityVisPlot_2D_plotly Man page
cellProximityVisPlot_3D_plotly Man page
changeGiottoInstructions Man page Source code
clusterCells Man page
createGiottoInstructions Man page Source code
createGiottoObject Man page Source code
createHeatmap_DT Man page Source code
createNearestNetwork Man page Source code
createSpatialGrid Man page
createSpatialGrid_2D Man page
createSpatialGrid_3D Man page
createSpatialNetwork Man page Source code
create_average_DT Man page Source code
create_average_detection_DT Man page Source code
create_cell_type_random_cell_IDs Man page
create_cluster_matrix Man page
create_dimObject Man page Source code
decide_cluster_order Man page Source code
detectSpatialPatterns Man page
dimGenePlot2D Man page
dimPlot2D Man page
direction_test Man page
direction_test_CPG Man page
doHMRF Man page Source code
doHclust Man page
doKmeans Man page
doLeidenCluster Man page Source code
doLeidenSubCluster Man page
doLouvainCluster Man page Source code
doLouvainCluster_community Man page Source code
doLouvainCluster_multinet Man page Source code
doLouvainSubCluster Man page
doLouvainSubCluster_community Man page
doLouvainSubCluster_multinet Man page
doRandomWalkCluster Man page Source code
doSNNCluster Man page Source code
dt_to_matrix Man page
exportGiottoViewer Man page Source code
exprOnlyCellCellcommunicationScores Man page
extended_gini_fun Man page Source code
extractNearestNetwork Man page
fDataDT Man page Source code
filterCombinations Man page Source code
filterDistributions Man page Source code
filterGiotto Man page
findGiniMarkers Man page Source code
findGiniMarkers_one_vs_all Man page
findMarkers Man page
findMarkers_one_vs_all Man page
findMastMarkers Man page
findMastMarkers_one_vs_all Man page
findScranMarkers Man page Source code
findScranMarkers_one_vs_all Man page Source code
find_grid_2D Man page Source code
find_grid_3D Man page Source code
find_grid_x Man page Source code
find_grid_y Man page
find_grid_z Man page
fish_function Man page Source code
fish_function2 Man page Source code
general_save_function Man page Source code
getCellProximityGeneScores Man page
getClusterSimilarity Man page
getDendrogramSplits Man page
getDistinctColors Man page Source code
getGeneToGeneSelection Man page
get_cell_to_cell_sorted_name_conversion Man page
get_interaction_gene_enrichment Man page
get_specific_interaction_gene_enrichment Man page
ggplot_save_function Man page Source code
giotto Man page
giotto-class Man page
iterCluster Man page
iterLeidenCluster Man page
iterLouvainCluster Man page
iterLouvainCluster_community Man page
iterLouvainCluster_multinet Man page
kmeans_binarize Man page Source code
loadHMRF Man page
make_simulated_network Man page Source code
mergeClusters Man page
mygini_fun Man page Source code
nnDT_to_kNN Man page
node_clusters Man page
normalizeGiotto Man page
pDataDT Man page Source code
plotCPGscores Man page
plotGTGscores Man page
plotHeatmap Man page Source code
plotMetaDataHeatmap Man page Source code
plotPCA Man page
plotPCA_2D Man page
plotTSNE Man page
plotTSNE_2D Man page
plotUMAP Man page
plotUMAP_2D Man page
plot_network_layer_ggplot Man page
plot_point_layer_ggplot Man page
plot_spat_point_layer_ggplot Man page
plotly_axis_scale_2D Man page Source code
plotly_axis_scale_3D Man page Source code
plotly_grid Man page Source code
plotly_network Man page Source code
print.giotto Man page
rank_binarize Man page Source code
readGiottoInstructions Man page Source code
removeCellAnnotation Man page
removeGeneAnnotation Man page
runPCA Man page Source code
runUMAP Man page Source code
runtSNE Man page Source code
selectPatternGenes Man page
select_expression_values Man page Source code
show,giotto-method Man page
showCPGscores Man page
showClusterDendrogram Man page Source code
showClusterHeatmap Man page Source code
showGTGscores Man page
showGeneExpressionProximityScore Man page
showGiottoInstructions Man page Source code
showIntExpressionProximityScore Man page
showPattern Man page
showPattern2D Man page
showPatternGenes Man page
showProcessingSteps Man page
showTopGeneToGene Man page
signPCA Man page Source code
spatDimGenePlot2D Man page
spatDimPlot2D Man page
spatGenePlot2D Man page
spatPlot2D Man page
specificCellCellcommunicationScores Man page
split_dendrogram_in_two Man page
stitchFieldCoordinates Man page Source code
subClusterCells Man page
subsetGiotto Man page Source code
viewHMRFresults Man page
viewHMRFresults2D Man page
violinPlot Man page Source code
visDimGenePlot Man page
visDimGenePlot_2D_ggplot Man page
visDimGenePlot_3D_plotly Man page
visDimPlot Man page
visDimPlot_2D_ggplot Man page Source code
visDimPlot_2D_plotly Man page Source code
visDimPlot_3D_plotly Man page
visForceLayoutPlot Man page
visGenePlot Man page Source code
visGenePlot_2D_ggplot Man page Source code
visGenePlot_3D_plotly Man page Source code
visPlot Man page Source code
visPlot_2D_ggplot Man page Source code
visPlot_2D_plotly Man page Source code
visPlot_3D_plotly Man page Source code
visSpatDimGenePlot Man page
visSpatDimGenePlot_2D Man page
visSpatDimGenePlot_3D Man page
visSpatDimPlot Man page
visSpatDimPlot_2D Man page
visSpatDimPlot_3D Man page
writeHMRFresults Man page
write_giotto_viewer_annotation Man page Source code
write_giotto_viewer_dim_reduction Man page Source code
RubD/Giotto documentation built on Nov. 19, 2019, 2:48 a.m.