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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(HeatmapCNR)
export(addBinInfo)
export(addCells)
export(addGeneInfo)
export(addInfo)
export(addPheno)
export(addQC)
export(add_in_silico_root)
export(avg_num_alleles_per_locus)
export(binary.X)
export(binary.cnr)
export(binaryDDRC)
export(buildCNR)
export(cbioportal_copy_number_states)
export(chr_breaks)
export(chr_colors)
export(cluster_heterogeneity)
export(cnr_data_type)
export(create_chromosome_annotation)
export(doKSpectral)
export(estimate_joint_effects)
export(excludeCells)
export(expand2genes)
export(export_cnr)
export(export_pval_igv)
export(genotype_vdj)
export(get_alteration_frequencies)
export(get_cluster_profiles)
export(histo_logit)
export(histo_logit_cov)
export(keepCells)
export(list_gene_symbols)
export(list_genes_in_region)
export(lookupCN)
export(mapd)
export(mark.genes)
export(maximum.percentage)
export(mid_chr)
export(minimum.intersect)
export(nbins)
export(ncells)
export(ngenes)
export(npheno)
export(optClust)
export(order_bins)
export(order_genes)
export(parctan)
export(phylo_cnr)
export(phylo_ddrc)
export(plotCL)
export(plot_ccp)
export(plot_cn_correlations)
export(plot_effect)
export(plot_frequencies)
export(plot_lr)
export(plot_sK)
export(proportion_of_polymorphic_loci)
export(pull_gene_copy_numbers)
export(pull_gene_details)
export(rank_clones)
export(rle_ddrc)
export(roundCNR)
export(run_consensus_clustering)
export(seg2bins)
export(setBrayClusters)
export(setKcc)
export(split_cnr)
export(subsetCNR)
export(summary_cnr)
export(sync_cnr)
export(vdjBrayClust)
export(vdjHeatmap)
export(vdjPlotClust)
import(ComplexHeatmap)
import(SCclust)
import(dplyr)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_mark)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,findOverlaps)
importFrom(IRanges,IRanges)
importFrom(ape,as.phylo)
importFrom(ape,fastme.bal)
importFrom(ape,fastme.ols)
importFrom(ape,nj)
importFrom(ape,root)
importFrom(ape,write.tree)
importFrom(assertthat,assert_that)
importFrom(assertthat,is.string)
importFrom(circlize,colorRamp2)
importFrom(dplyr,"%>%")
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,tibble)
importFrom(glmnet,cv.glmnet)
importFrom(glmnet,glmnet)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,segments)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(qvalue,qvalue)
importFrom(reshape2,melt)
importFrom(stats,coef)
importFrom(stats,complete.cases)
importFrom(stats,cutree)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,predict)
importFrom(stats,sd)
importFrom(tidyr,pivot_wider)
importFrom(utils,head)
importFrom(utils,read.delim)
importFrom(utils,write.table)
importFrom(vegan,diversity)
importFrom(vegan,vegdist)