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Giotto Suite 3.2.0 documentation
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General

  • Branches
  • Getting Started
  • Documentation
    • installGiottoEnvironment
    • removeGiottoEnvironment
    • checkGiottoEnvironment
    • createGiottoInstructions
    • readGiottoInstructions
    • showGiottoInstructions
    • changeGiottoInstructions
    • replaceGiottoInstructions
    • getSpatialDataset
    • readExprMatrix
    • get10Xmatrix
    • get10Xmatrix_h5
    • stitchFieldCoordinates
    • stitchTileCoordinates
    • readPolygonFilesVizgen
    • readPolygonFilesVizgenHDF5
    • estimateImageBg
    • changeImageBg
    • createGiottoImage
    • addGiottoImage
    • addGiottoImageToSpatPlot
    • showGiottoImageNames
    • updateGiottoImage
    • get_giottoImage
    • plotGiottoImage
    • set_giottoImage
    • addGiottoLargeImage
    • createGiottoLargeImage
    • createGiottoLargeImageList
    • cropGiottoLargeImage
    • updateGiottoLargeImage
    • writeGiottoLargeImage
    • stitchGiottoLargeImage
    • convertGiottoLargeImageToMG
    • addGiottoImageMG
    • updateGiottoImageMG
    • distGiottoImage
    • reconnectGiottoImage
    • registerImagesFIJI
    • registerGiottoObjectList
    • createGiottoObject
    • createGiottoVisiumObject
    • createGiottoObjectSubcellular
    • createGiottoCosMxObject
    • pDataDT
    • fDataDT
    • showProcessingSteps
    • calculateMetaTable
    • calculateMetaTableCells
    • combineMetadata
    • createMetafeats
    • findNetworkNeighbors
    • objHistory
    • get_expression_values
    • set_expression_values
    • get_spatial_locations
    • set_spatial_locations
    • get_dimReduction
    • set_dimReduction
    • get_NearestNetwork
    • set_NearestNetwork
    • get_spatialNetwork
    • set_spatialNetwork
    • get_spatialGrid
    • set_spatialGrid
    • get_polygon_info
    • set_polygon_info
    • get_feature_info
    • set_feature_info
    • get_spatial_enrichment
    • set_spatial_enrichment
    • showGiottoExpression
    • showGiottoSpatLocs
    • showGiottoDimRed
    • showGiottoSpatNetworks
    • showGiottoSpatGrids
    • showGiottoSpatialInfo
    • showGiottoFeatInfo
    • showGiottoSpatEnrichments
    • showGiottoNearestNetworks
    • showGrids
    • showNetworks
    • filterGiotto
    • filterCombinations
    • filterDistributions
    • subsetGiotto
    • subsetGiottoLocs
    • subsetGiottoLocsMulti
    • joinGiottoObjects
    • normalizeGiotto
    • adjustGiottoMatrix
    • annotateGiotto
    • removeCellAnnotation
    • removeFeatAnnotation
    • addCellMetadata
    • addFeatMetadata
    • addFeatStatistics
    • addCellStatistics
    • addStatistics
    • addFeatsPerc
    • addCellIntMetadata
    • processGiotto
    • calculateHVF
    • signPCA
    • screePlot
    • jackstrawPlot
    • runPCA
    • runUMAP
    • runtSNE
    • runGiottoHarmony
    • runWNN
    • createNearestNetwork
    • addNetworkLayout
    • clusterCells
    • doLeidenCluster
    • doLouvainCluster
    • doKmeans
    • doHclust
    • doRandomWalkCluster
    • doSNNCluster
    • subClusterCells
    • doLeidenSubCluster
    • doLouvainSubCluster
    • getClusterSimilarity
    • mergeClusters
    • getDendrogramSplits
    • findMarkers
    • findMarkers_one_vs_all
    • findGiniMarkers
    • findGiniMarkers_one_vs_all
    • findScranMarkers
    • findScranMarkers_one_vs_all
    • findMastMarkers
    • findMastMarkers_one_vs_all
    • showClusterHeatmap
    • showClusterDendrogram
    • plotHeatmap
    • plotMetaDataHeatmap
    • plotMetaDataCellsHeatmap
    • violinPlot
    • makeSignMatrixPAGE
    • makeSignMatrixRank
    • runSpatialEnrich
    • runPAGEEnrich
    • runRankEnrich
    • runHyperGeometricEnrich
    • makeSignMatrixDWLSfromMatrix
    • makeSignMatrixDWLS
    • runSpatialDeconv
    • runDWLSDeconv
    • spatDeconvPlot
    • spatNetwDistributionsDistance
    • spatNetwDistributionsKneighbors
    • spatNetwDistributions
    • createSpatialDelaunayNetwork
    • plotStatDelaunayNetwork
    • createSpatialKNNnetwork
    • createSpatialFeaturesKNNnetwork
    • createSpatialNetwork
    • annotateSpatialNetwork
    • annotateSpatialGrid
    • createSpatialGrid
    • createSpatialDefaultGrid
    • binSpectSingleMatrix
    • binSpectMultiMatrix
    • binSpectSingle
    • binSpectMulti
    • binSpect
    • spatialDE
    • spatialAEH
    • trendSceek
    • spark
    • simulateOneGenePatternGiottoObject
    • runPatternSimulation
    • clusterSpatialCorFeats
    • detectSpatialCorFeats
    • detectSpatialCorFeatsMatrix
    • detectSpatialPatterns
    • heatmSpatialCorFeats
    • showSpatialCorFeats
    • showPattern2D
    • showPattern3D
    • rankSpatialCorGroups
    • combineSpatialCellFeatureInfo
    • combineSpatialCellMetadataInfo
    • doHMRF
    • loadHMRF
    • viewHMRFresults
    • writeHMRFresults
    • addHMRF
    • viewHMRFresults2D
    • viewHMRFresults3D
    • getDistinctColors
    • showSaveParameters
    • dimPlot
    • dimPlot2D
    • plotUMAP
    • plotUMAP_2D
    • plotTSNE
    • plotTSNE_2D
    • plotPCA
    • plotPCA_2D
    • dimFeatPlot2D
    • dimCellPlot2D
    • spatPlot2D
    • spatCellPlot2D
    • spatFeatPlot2D
    • spatDimPlot2D
    • spatDimCellPlot2D
    • spatDimFeatPlot2D
    • dimPlot3D
    • plotUMAP_3D
    • plotTSNE_3D
    • plotPCA_3D
    • spatPlot3D
    • spatDimPlot3D
    • createCrossSection
    • crossSectionGenePlot
    • crossSectionPlot
    • crossSectionGenePlot3D
    • crossSectionPlot3D
    • insertCrossSectionSpatPlot3D
    • insertCrossSectionGenePlot3D
    • cellProximityEnrichment
    • cellProximityBarplot
    • cellProximityHeatmap
    • cellProximityNetwork
    • cellProximitySpatPlot
    • cellProximitySpatPlot3D
    • specificCellCellcommunicationScores
    • findInteractionChangedFeats
    • findICF
    • filterInteractionChangedFeats
    • filterICF
    • plotInteractionChangedFeats
    • plotICF
    • plotCellProximityFeats
    • plotCPF
    • combineInteractionChangedFeats
    • combineICF
    • plotCombineInteractionChangedFeats
    • plotCombineICF
    • combCCcom
    • exprCellCellcom
    • spatCellCellcom
    • plotCCcomDotplot
    • plotRankSpatvsExpr
    • plotRecovery
    • plotCCcomHeatmap
    • plotCombineCellCellCommunication
    • plotCombineCCcom
    • addCellsFromPolygon
    • addGiottoPoints
    • addGiottoPoints3D
    • addGiottoPolygons
    • addSpatialCentroidLocations
    • addSpatialCentroidLocationsLayer
    • calculateOverlapParallel
    • calculateOverlapPolygonImages
    • calculateOverlapRaster
    • calculateOverlapSerial
    • combineCellData
    • combineFeatureData
    • combineFeatureOverlapData
    • createGiottoPoints
    • createGiottoPolygonsFromDfr
    • createGiottoPolygonsFromMask
    • overlapToMatrix
    • overlapImagesToMatrix
    • overlapToMatrixMultiPoly
    • smoothGiottoPolygons
    • spatInSituPlotDensity
    • spatInSituPlotHex
    • spatInSituPlotPoints
    • doCellSegmentation
    • doScrubletDetect
    • cellProximitySpatPlot2D
    • cellProximityVisPlot
    • comparePolygonExpression
    • getCellsFromPolygon
    • plotInteractivePolygons
    • seuratToGiotto
    • giottoToSeurat
    • giottoToSpatialExperiment
  • Contribute

Tutorials

  • Tutorials
    • Stereo-Seq Mouse Embryo
    • Seq-Scope Mouse Liver
    • Xenium Breast Cancer
    • Nanostring CosMx Lung
    • MERFISH
    • Vizgen Brain
    • Visium Mouse Kidney
    • Visium Mouse Brain
    • Visium Prostate Integration
    • CytAssist Human Lung Cancer (FFPE)
    • Mini SeqFISH
    • SeqFISH+ Cortex
    • osmFISH SS Cortex
    • Resolve Biosciences
    • CODEX Spleen
    • scRNA-seq Prostate
    • scRNA-seq Integration
    • Other technologies

Try Giotto in the Cloud

  • Terra.bio
  • Docker

Issues

  • FAQs
  • Troubleshooting
  • Report a Bug

Updates

  • Giotto Suite 3.2.0 (2023-02-02)
  • Giotto Suite 3.1.0 (2202-12-01)
  • Giotto Suite 3.0.1 (2022-11-20)
  • Giotto Suite 3.0.0 (2022-11-18)
  • Giotto Suite 2.1.0 (2202-11-09)
  • Giotto Suite 2.0.0.998
  • News
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News#

Date:

2022-11-11

Giotto receives CZI EOSS award#

November 11, 2022

Giotto receives grant from the Essential Open Source Software for Science (EOSS) program from the Chan Zuckerberg Initiative (CZI) in Round 5.

Giotto featured in Current Protocols#

April 5, 2022

Read the publication here

Spatial -omics review published in Genome Research#

October 31, 2021

Read the publication here

Giotto published in Genome Biology#

March 08, 2021

Read the publication here

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Giotto Suite 3.2.0 (2023-02-02)
Copyright © 2022, Ruben Dries and Guo-Cheng Yuan
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On this page
  • News
    • Giotto receives CZI EOSS award
    • Giotto featured in Current Protocols
    • Spatial -omics review published in Genome Research
    • Giotto published in Genome Biology