# Generated by roxygen2: do not edit by hand

S3method(optimizeALS,liger)
S3method(optimizeALS,list)
S3method(quantile_norm,liger)
S3method(quantile_norm,list)
export(calcARI)
export(calcAgreement)
export(calcAlignment)
export(calcAlignmentPerCluster)
export(calcDatasetSpecificity)
export(calcNormLoadings)
export(calcPurity)
export(convertOldLiger)
export(createLiger)
export(getFactorMarkers)
export(getGeneValues)
export(getProportionMito)
export(imputeKNN)
export(ligerToSeurat)
export(linkGenesAndPeaks)
export(louvainCluster)
export(makeFeatureMatrix)
export(makeInteractTrack)
export(makeRiverplot)
export(mergeH5)
export(normalize)
export(online_iNMF)
export(optimizeALS)
export(optimizeNewData)
export(optimizeNewK)
export(optimizeNewLambda)
export(optimizeSubset)
export(plotByDatasetAndCluster)
export(plotClusterFactors)
export(plotClusterProportions)
export(plotFactors)
export(plotFeature)
export(plotGene)
export(plotGeneLoadings)
export(plotGeneViolin)
export(plotGenes)
export(plotWordClouds)
export(quantileAlignSNF)
export(quantile_norm)
export(read10X)
export(readSubset)
export(removeMissingObs)
export(reorganizeLiger)
export(restoreOnlineLiger)
export(runGSEA)
export(runTSNE)
export(runUMAP)
export(runWilcoxon)
export(scaleNotCenter)
export(selectGenes)
export(seuratToLiger)
export(subsetLiger)
export(suggestK)
export(suggestLambda)
exportClasses(liger)
import(Matrix)
import(doParallel)
import(hdf5r)
import(parallel)
import(patchwork)
importFrom(FNN,get.knn)
importFrom(FNN,get.knnx)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Rcpp,evalCpp)
importFrom(Rtsne,Rtsne)
importFrom(cowplot,draw_grob)
importFrom(cowplot,plot_grid)
importFrom(cowplot,theme_cowplot)
importFrom(dplyr,"%>%")
importFrom(dplyr,group_by)
importFrom(dplyr,group_cols)
importFrom(dplyr,mutate_at)
importFrom(dplyr,summarize)
importFrom(dplyr,vars)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_viridis_c)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,heat.colors)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,barplot)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,title)
importFrom(grid,gpar)
importFrom(grid,roundrectGrob)
importFrom(grid,unit)
importFrom(ica,icafast)
importFrom(irlba,prcomp_irlba)
importFrom(mclust,adjustedRandIndex)
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(plyr,mapvalues)
importFrom(plyr,rbind.fill.matrix)
importFrom(rlang,.data)
importFrom(scattermore,geom_scattermore)
importFrom(stats,approxfun)
importFrom(stats,complete.cases)
importFrom(stats,heatmap)
importFrom(stats,loadings)
importFrom(stats,median)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,wilcox.test)
importFrom(utils,capture.output)
importFrom(utils,file_test)
importFrom(utils,packageVersion)
importFrom(utils,read.csv2)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
useDynLib(rliger)
