NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export(PAGEEnrich)
export(addCellIntMetadata)
export(addCellMetadata)
export(addCellStatistics)
export(addGeneMetadata)
export(addGeneStatistics)
export(addGenesPerc)
export(addGiottoImage)
export(addGiottoImageToSpatPlot)
export(addHMRF)
export(addHMRF_V2)
export(addNetworkLayout)
export(addStatistics)
export(adjustGiottoMatrix)
export(anndataToGiotto)
export(annotateGiotto)
export(annotateSpatialGrid)
export(annotateSpatialNetwork)
export(binSpect)
export(binSpectMulti)
export(binSpectSingle)
export(calculateHVG)
export(calculateMetaTable)
export(calculateMetaTableCells)
export(cellProximityBarplot)
export(cellProximityEnrichment)
export(cellProximityEnrichmentEachSpot)
export(cellProximityEnrichmentSpots)
export(cellProximityHeatmap)
export(cellProximityNetwork)
export(cellProximitySpatPlot)
export(cellProximitySpatPlot2D)
export(cellProximitySpatPlot3D)
export(cellProximityVisPlot)
export(changeGiottoInstructions)
export(changeImageBg)
export(checkAndFixSpatialGenes)
export(checkGiottoEnvironment)
export(chooseAvailableSpatialGenes)
export(clusterCells)
export(clusterSpatialCorGenes)
export(combCCcom)
export(combineCPG)
export(combineCellProximityGenes)
export(combineICG)
export(combineInteractionChangedGenes)
export(combineMetadata)
export(convertEnsemblToGeneSymbol)
export(createCrossSection)
export(createGiottoImage)
export(createGiottoInstructions)
export(createGiottoObject)
export(createGiottoVisiumObject)
export(createMetagenes)
export(createNearestNetwork)
export(createRegZStackGobject)
export(createSpatialDefaultGrid)
export(createSpatialDelaunayNetwork)
export(createSpatialEnrich)
export(createSpatialGrid)
export(createSpatialKNNnetwork)
export(createSpatialNetwork)
export(create_crossSection_object)
export(crossSectionGenePlot)
export(crossSectionGenePlot3D)
export(crossSectionPlot)
export(crossSectionPlot3D)
export(detectSpatialCorGenes)
export(dimCellPlot)
export(dimCellPlot2D)
export(dimGenePlot)
export(dimGenePlot2D)
export(dimGenePlot3D)
export(dimPlot)
export(dimPlot2D)
export(dimPlot3D)
export(doHMRF)
export(doHMRF_V2)
export(doHclust)
export(doKmeans)
export(doLeidenCluster)
export(doLeidenSubCluster)
export(doLouvainCluster)
export(doLouvainSubCluster)
export(doRandomWalkCluster)
export(doSNNCluster)
export(estimateImageBg)
export(explainGiottoInstructions)
export(exportGiottoViewer)
export(exprCellCellcom)
export(fDataDT)
export(filterCPG)
export(filterCellProximityGenes)
export(filterCombinations)
export(filterDistributions)
export(filterGiotto)
export(filterICG)
export(filterICGSpot)
export(filterInteractionChangedGenes)
export(filterSpatialGenes)
export(findCPG)
export(findCellProximityGenes)
export(findGiniMarkers)
export(findGiniMarkers_one_vs_all)
export(findICG)
export(findICGSpot)
export(findInteractionChangedGenes)
export(findMarkers)
export(findMarkers_one_vs_all)
export(findMastMarkers)
export(findMastMarkers_one_vs_all)
export(findNetworkNeighbors)
export(findScranMarkers)
export(findScranMarkers_one_vs_all)
export(geneExpDWLS)
export(get10Xmatrix)
export(get10Xmatrix_h5)
export(getClusterSimilarity)
export(getDendrogramSplits)
export(getDistinctColors)
export(getGiottoImage)
export(getSpatialDataset)
export(giotto)
export(heatmSpatialCorGenes)
export(hyperGeometricEnrich)
export(initHMRF_V2)
export(insertCrossSectionGenePlot3D)
export(insertCrossSectionSpatPlot3D)
export(installGiottoEnvironment)
export(jackstrawPlot)
export(loadHMRF)
export(makeSignMatrixDWLS)
export(makeSignMatrixDWLSfromMatrix)
export(makeSignMatrixPAGE)
export(makeSignMatrixRank)
export(mergeClusters)
export(normalizeGiotto)
export(pDataDT)
export(plotCCcomDotplot)
export(plotCCcomHeatmap)
export(plotCPG)
export(plotCellProximityGenes)
export(plotCellProximityGenesSpot)
export(plotCombineCCcom)
export(plotCombineCPG)
export(plotCombineCellCellCommunication)
export(plotCombineCellProximityGenes)
export(plotCombineICG)
export(plotCombineInteractionChangedGenes)
export(plotGiottoImage)
export(plotHeatmap)
export(plotICG)
export(plotICGSpot)
export(plotInteractionChangedGenes)
export(plotMetaDataCellsHeatmap)
export(plotMetaDataHeatmap)
export(plotPCA)
export(plotPCA_2D)
export(plotPCA_3D)
export(plotRankSpatvsExpr)
export(plotRecovery)
export(plotStatDelaunayNetwork)
export(plotTSNE)
export(plotTSNE_2D)
export(plotTSNE_3D)
export(plotUMAP)
export(plotUMAP_2D)
export(plotUMAP_3D)
export(plot_spat_voronoi_layer_ggplot)
export(processGiotto)
export(rankEnrich)
export(rankSpatialCorGroups)
export(readExprMatrix)
export(readGiottoInstructions)
export(removeCellAnnotation)
export(removeGeneAnnotation)
export(removeGiottoEnvironment)
export(replaceGiottoInstructions)
export(runDWLSDeconv)
export(runHyperGeometricEnrich)
export(runPAGEEnrich)
export(runPCA)
export(runPatternSimulation)
export(runRankEnrich)
export(runSpatialDeconv)
export(runSpatialEnrich)
export(runUMAP)
export(runtSNE)
export(screePlot)
export(showClusterDendrogram)
export(showClusterHeatmap)
export(showGiottoImageNames)
export(showGiottoInstructions)
export(showGrids)
export(showNetworks)
export(showProcessingSteps)
export(showSaveParameters)
export(showSpatialCorGenes)
export(signPCA)
export(silhouetteRank)
export(simulateOneGenePatternGiottoObject)
export(spark)
export(spatCellCellcom)
export(spatCellCellcomSpots)
export(spatCellPlot)
export(spatCellPlot2D)
export(spatDeconvPlot)
export(spatDimCellPlot)
export(spatDimCellPlot2D)
export(spatDimGenePlot)
export(spatDimGenePlot2D)
export(spatDimGenePlot3D)
export(spatDimPlot)
export(spatDimPlot2D)
export(spatDimPlot3D)
export(spatGenePlot)
export(spatGenePlot2D)
export(spatGenePlot3D)
export(spatNetwDistributions)
export(spatNetwDistributionsDistance)
export(spatNetwDistributionsKneighbors)
export(spatPlot)
export(spatPlot2D)
export(spatPlot3D)
export(spatialAEH)
export(spatialDE)
export(specificCellCellcommunicationScores)
export(stitchFieldCoordinates)
export(stitchTileCoordinates)
export(subClusterCells)
export(subsetGiotto)
export(subsetGiottoLocs)
export(trendSceek)
export(updateGiottoImage)
export(viewHMRFresults)
export(viewHMRFresults2D)
export(viewHMRFresults3D)
export(viewHMRFresults_V2)
export(violinPlot)
export(writeHMRFresults)
exportClasses(giotto)
import(data.table)
import(ggplot2)
import(utils)
importFrom(magrittr,"%>%")
importFrom(methods,new)