scMetaLink/NAMESPACE at main · WaveoffBioMed/scMetaLink · GitHub

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# Generated by roxygen2: do not edit by hand

export(aggregateByPathway)
export(checkLactateGenes)
export(citationScMetaLink)
export(compareCommunication)
export(computeCommunication)
export(computeSpatialCommunication)
export(createScMetaLink)
export(createScMetaLinkFromSCE)
export(createScMetaLinkFromSeurat)
export(createScMetaLinkFromSeuratSpatial)
export(createScMetaLinkFromSpatial)
export(enrichPathways)
export(exportResults)
export(filterSignificantInteractions)
export(getCommunicationMatrix)
export(getCommunicationScores)
export(getDatabaseInfo)
export(getLactateGenes)
export(getLactateSignalingSummary)
export(getMetaboliteReceptors)
export(getParameters)
export(getPathwayAggregated)
export(getPathwayCommunicationMatrix)
export(getPathwayMetaboliteNetwork)
export(getPathwayMetabolites)
export(getProductionScores)
export(getSensingScores)
export(getSignificantInteractions)
export(getSpatialDistanceStats)
export(getSpatialLactateHotspots)
export(getSummaryStats)
export(getTopLactateProducers)
export(getTopLactateSensors)
export(getTopProducers)
export(getTopSensors)
export(identifyCellTypeSpecificMetabolites)
export(identifyCommunicationHotspots)
export(inferLactateSignaling)
export(inferProduction)
export(inferSensing)
export(inferSpatialLactateSignaling)
export(listGenes)
export(listMetabolites)
export(listTopPathways)
export(loadScMetaLink)
export(plotCommunicationCircle)
export(plotCommunicationHeatmap)
export(plotCommunicationNetwork)
export(plotDifferentialCommunication)
export(plotEnrichedPathways)
export(plotLactatePathwayComparison)
export(plotLactateSignaling)
export(plotMetaboliteProfile)
export(plotPathwayCommunication)
export(plotSpatialCellTypes)
export(plotSpatialCommunicationNetwork)
export(plotSpatialComparison)
export(plotSpatialDistanceDistribution)
export(plotSpatialFeature)
export(plotSpatialHotspots)
export(plotSpatialLactate)
export(plotTopInteractions)
export(runScMetaLink)
export(runScMetaLinkSeurat)
export(saveScMetaLink)
export(searchGene)
export(searchMetabolite)
export(summarizeCommunicationPairs)
export(summarizePathwayActivity)
exportClasses(scMetaLink)
exportMethods(getCommunicationScores)
exportMethods(getParameters)
exportMethods(getPathwayAggregated)
exportMethods(getProductionScores)
exportMethods(getSensingScores)
exportMethods(getSignificantInteractions)
exportMethods(show)
import(ggplot2)
import(methods)
importFrom(Matrix,Matrix)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,title)
importFrom(stats,aggregate)
importFrom(stats,dist)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,phyper)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)