NAMESPACE

# Generated by roxygen2: do not edit by hand

export(CreateInfercnvObject)
export(add_to_seurat)
export(apply_median_filtering)
export(color.palette)
export(filterHighPNormals)
export(inferCNVBayesNet)
export(plot_cnv)
export(plot_per_group)
export(plot_subclusters)
export(run)
export(sample_object)
exportClasses(MCMC_inferCNV)
exportClasses(infercnv)
import(RColorBrewer)
import(argparse)
import(coda)
import(doParallel)
import(fitdistrplus)
import(foreach)
import(futile.logger)
import(future)
import(ggplot2)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,mean)
importFrom(BiocGenerics,t)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,sparseMatrix)
importFrom(RANN,nn2)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,RunPCA)
importFrom(Seurat,ScaleData)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,start)
importFrom(ape,as.phylo)
importFrom(ape,drop.tip)
importFrom(ape,read.tree)
importFrom(ape,write.tree)
importFrom(caTools,runmean)
importFrom(coin,oneway_test)
importFrom(coin,pvalue)
importFrom(digest,digest)
importFrom(dplyr,"%>%")
importFrom(dplyr,count)
importFrom(edgeR,estimateDisp)
importFrom(fastcluster,hclust)
importFrom(gplots,bluered)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(gridExtra,gtable_combine)
importFrom(gridExtra,marrangeGrob)
importFrom(gridExtra,tableGrob)
importFrom(gridExtra,ttheme_default)
importFrom(igraph,cluster_leiden)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(parallel,detectCores)
importFrom(parallelDist,parallelDist)
importFrom(phyclust,get.rooted.tree.height)
importFrom(reshape2,melt)
importFrom(rjags,coda.samples)
importFrom(rjags,jags.model)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,as.hclust)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,ecdf)
importFrom(stats,filter)
importFrom(stats,ks.test)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,nls)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,qgamma)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,rbinom)
importFrom(stats,rchisq)
importFrom(stats,reorder)
importFrom(stats,rgamma)
importFrom(stats,rlnorm)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,shapiro.test)
importFrom(stats,smooth.spline)
importFrom(stats,t.test)
importFrom(stats,update)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tidyr,gather)
importFrom(utils,capture.output)
importFrom(utils,flush.console)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.table)