# Generated by roxygen2: do not edit by hand

S3method("$",liger)
S3method("$<-",liger)
S3method("[",liger)
S3method("[",ligerDataset)
S3method("[[",liger)
S3method("[[<-",liger)
S3method("names<-",liger)
S3method(.DollarNames,liger)
S3method(alignFactors,Seurat)
S3method(alignFactors,liger)
S3method(as.liger,Seurat)
S3method(as.liger,SingleCellExperiment)
S3method(as.liger,dgCMatrix)
S3method(as.ligerDataset,Seurat)
S3method(as.ligerDataset,SingleCellExperiment)
S3method(as.ligerDataset,default)
S3method(as.ligerDataset,ligerDataset)
S3method(as.ligerDataset,matrix)
S3method(c,liger)
S3method(cbind,ligerDataset)
S3method(centroidAlign,Seurat)
S3method(centroidAlign,liger)
S3method(closeAllH5,liger)
S3method(closeAllH5,ligerDataset)
S3method(fortify,liger)
S3method(length,liger)
S3method(lengths,liger)
S3method(names,liger)
S3method(normalize,Seurat)
S3method(normalize,dgCMatrix)
S3method(normalize,liger)
S3method(normalize,ligerDataset)
S3method(normalize,matrix)
S3method(plotSpatial2D,liger)
S3method(plotSpatial2D,ligerSpatialDataset)
S3method(quantileNorm,Seurat)
S3method(quantileNorm,liger)
S3method(runCINMF,Seurat)
S3method(runCINMF,liger)
S3method(runINMF,Seurat)
S3method(runINMF,liger)
S3method(runIntegration,Seurat)
S3method(runIntegration,liger)
S3method(runOnlineINMF,Seurat)
S3method(runOnlineINMF,liger)
S3method(runUINMF,liger)
S3method(scaleNotCenter,Seurat)
S3method(scaleNotCenter,dgCMatrix)
S3method(scaleNotCenter,liger)
S3method(scaleNotCenter,ligerDataset)
S3method(scaleNotCenter,ligerMethDataset)
S3method(selectGenes,Seurat)
S3method(selectGenes,liger)
S3method(writeH5,default)
S3method(writeH5,dgCMatrix)
S3method(writeH5,liger)
S3method(writeH5,ligerDataset)
export("%<>%")
export("%>%")
export("cellMeta<-")
export("coordinate<-")
export("dataset<-")
export("datasets<-")
export("defaultCluster<-")
export("defaultDimRed<-")
export("dimRed<-")
export("dimReds<-")
export("featureMeta<-")
export("h5fileInfo<-")
export("normData<-")
export("normPeak<-")
export("rawData<-")
export("rawPeak<-")
export("scaleData<-")
export("scaleUnsharedData<-")
export("varFeatures<-")
export("varUnsharedFeatures<-")
export(alignFactors)
export(as.liger)
export(as.ligerDataset)
export(calcARI)
export(calcAgreement)
export(calcAlignment)
export(calcDatasetSpecificity)
export(calcNMI)
export(calcPurity)
export(cellMeta)
export(centroidAlign)
export(closeAllH5)
export(commandDiff)
export(commands)
export(convertOldLiger)
export(coordinate)
export(createH5LigerDataset)
export(createLiger)
export(createLigerDataset)
export(dataset)
export(datasets)
export(defaultCluster)
export(defaultDimRed)
export(dimRed)
export(dimReds)
export(downsample)
export(exportInteractTrack)
export(featureMeta)
export(getFactorMarkers)
export(getH5File)
export(getMatrix)
export(getProportionMito)
export(h5fileInfo)
export(importBMMC)
export(importCGE)
export(importPBMC)
export(imputeKNN)
export(is.newLiger)
export(isH5Liger)
export(ligerATACDataset)
export(ligerCommand)
export(ligerMethDataset)
export(ligerRNADataset)
export(ligerSpatialDataset)
export(ligerToSeurat)
export(linkGenesAndPeaks)
export(louvainCluster)
export(makeFeatureMatrix)
export(makeInteractTrack)
export(makeRiverplot)
export(mapCellMeta)
export(mergeDenseAll)
export(mergeH5)
export(mergeSparseAll)
export(modalOf)
export(normData)
export(normPeak)
export(normalize)
export(normalizePeak)
export(online_iNMF)
export(optimizeALS)
export(optimizeNewData)
export(optimizeNewK)
export(optimizeNewLambda)
export(optimizeSubset)
export(plotBarcodeRank)
export(plotByDatasetAndCluster)
export(plotCellViolin)
export(plotClusterDimRed)
export(plotClusterFactorDot)
export(plotClusterGeneDot)
export(plotClusterGeneViolin)
export(plotClusterProportions)
export(plotDatasetDimRed)
export(plotDensityDimRed)
export(plotDimRed)
export(plotEnhancedVolcano)
export(plotFactorDimRed)
export(plotFactorHeatmap)
export(plotGODot)
export(plotGeneDetectedViolin)
export(plotGeneDimRed)
export(plotGeneHeatmap)
export(plotGeneLoadingRank)
export(plotGeneLoadings)
export(plotGeneViolin)
export(plotGroupClusterDimRed)
export(plotMarkerHeatmap)
export(plotPairwiseDEGHeatmap)
export(plotPeakDimRed)
export(plotProportion)
export(plotProportionBar)
export(plotProportionBox)
export(plotProportionDot)
export(plotProportionPie)
export(plotSankey)
export(plotSpatial2D)
export(plotTotalCountViolin)
export(plotVarFeatures)
export(plotVolcano)
export(quantileAlignSNF)
export(quantileNorm)
export(quantile_norm)
export(rawData)
export(rawPeak)
export(read10X)
export(read10XATAC)
export(read10XFiles)
export(read10XRNA)
export(readLiger)
export(readSubset)
export(removeMissing)
export(removeMissingObs)
export(restoreH5Liger)
export(restoreOnlineLiger)
export(retrieveCellFeature)
export(reverseMethData)
export(runCINMF)
export(runCluster)
export(runDoubletFinder)
export(runGOEnrich)
export(runGSEA)
export(runGeneralQC)
export(runINMF)
export(runIntegration)
export(runMarkerDEG)
export(runOnlineINMF)
export(runPairwiseDEG)
export(runTSNE)
export(runUINMF)
export(runUMAP)
export(runWilcoxon)
export(scaleData)
export(scaleNotCenter)
export(scaleUnsharedData)
export(selectGenes)
export(selectGenesVST)
export(seuratToLiger)
export(subsetH5LigerDataset)
export(subsetLiger)
export(subsetLigerDataset)
export(subsetMemLigerDataset)
export(updateLigerObject)
export(varFeatures)
export(varUnsharedFeatures)
export(writeH5)
exportClasses(ligerATACDataset)
exportClasses(ligerCommand)
exportClasses(ligerDataset)
exportClasses(ligerMethDataset)
exportClasses(ligerRNADataset)
exportClasses(ligerSpatialDataset)
exportMethods("cellMeta<-")
exportMethods("coordinate<-")
exportMethods("dataset<-")
exportMethods("datasets<-")
exportMethods("defaultCluster<-")
exportMethods("defaultDimRed<-")
exportMethods("dimRed<-")
exportMethods("dimReds<-")
exportMethods("dimnames<-")
exportMethods("featureMeta<-")
exportMethods("h5fileInfo<-")
exportMethods("normData<-")
exportMethods("normPeak<-")
exportMethods("rawData<-")
exportMethods("rawPeak<-")
exportMethods("scaleData<-")
exportMethods("scaleUnsharedData<-")
exportMethods("varFeatures<-")
exportMethods("varUnsharedFeatures<-")
exportMethods(cellMeta)
exportMethods(commands)
exportMethods(coordinate)
exportMethods(dataset)
exportMethods(datasets)
exportMethods(defaultCluster)
exportMethods(defaultDimRed)
exportMethods(dim)
exportMethods(dimRed)
exportMethods(dimReds)
exportMethods(dimnames)
exportMethods(featureMeta)
exportMethods(getH5File)
exportMethods(getMatrix)
exportMethods(h5fileInfo)
exportMethods(normData)
exportMethods(normPeak)
exportMethods(rawData)
exportMethods(rawPeak)
exportMethods(scaleData)
exportMethods(scaleUnsharedData)
exportMethods(show)
exportMethods(varFeatures)
exportMethods(varUnsharedFeatures)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgTMatrix)
importClassesFrom(Matrix,dgeMatrix)
importClassesFrom(S4Vectors,DataFrame)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,summary)
importFrom(Matrix,t)
importFrom(Rcpp,evalCpp)
importFrom(ggplot2,fortify)
importFrom(lifecycle,deprecated)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(methods,new)
importFrom(methods,show)
importFrom(rlang,"%||%")
importFrom(rlang,.data)
importFrom(utils,.DollarNames)
useDynLib(rliger, .registration = TRUE)
