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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(ATAC_Wrapper)
export(AddDatatoplot_clustering)
export(AddDist)
export(AddDist_legacy)
export(AddHemSignature)
export(AddTree)
export(Add_AssignVariant)
export(Add_DepthMatrix)
export(Add_tree_cut)
export(BinaryDist)
export(CW_mgatk.read)
export(Clone_FinderMarker)
export(ComputeRejectRate)
export(ComputeRejectRate_legacy)
export(CountOverlap_Adj)
export(Create_mitoTracing)
export(Create_redeemR)
export(Create_redeemR_model)
export(DE.gettripple)
export(Datatoplots)
export(DepthSummary)
export(DistObjects)
export(DoDE)
export(FromDist2Graph)
export(Fun.enrich_withFC)
export(Fun.enrich_withFC.pvalue)
export(GEM_Wrapper)
export(GTSummary)
export(Get_Clonal_Variants)
export(LineageBiasPlot)
export(MakeAllNodes)
export(MakeDF4Regress)
export(MakeNN)
export(Make_AnnTable)
export(Make_Cells4Nodes)
export(Make_matrix)
export(Make_tree)
export(Make_tree_legacy)
export(MergeMtx)
export(Motifenrich.binom)
export(Multi_Wrapper)
export(MutationProfile.bulk)
export(NN2M)
export(ProgenyMapping)
export(ProgenyMapping_np)
export(Reclustering)
export(Reclustering_hm)
export(Run_Lin_regression)
export(Run_Lin_regression_poi)
export(Runplot_scale_2)
export(Runplot_scale_3)
export(SeuratLSIClustering)
export(Show_Consensus)
export(Subset_redeemR)
export(TREE)
export(Tomerge.col)
export(Tomerge_v2)
export(Translate_RNA2ATAC)
export(Translate_simple_ATAC2RNA)
export(Translate_simple_RNA2ATAC)
export(Vfilter_v3)
export(Vfilter_v4)
export(add_changes)
export(add_freq_raw)
export(add_hypermutable)
export(add_raw_fragment)
export(add_types)
export(binomialtest.msig.enrch_deplet)
export(clean_redeem)
export(clean_redeem_removehot)
export(convert_mitotracing_redeemR)
export(convert_variant)
export(get_hype_v2)
export(gsea_enrichmentheat)
export(make_ks_test_df)
export(make_position_df_3.5)
export(mitoTracing)
export(plot_depth)
export(plot_depth_legacy)
export(plot_npSummary)
export(plot_variant)
export(plot_variant_legacy)
export(quick_w_cosine)
export(quick_w_jaccard)
export(reconstruct_genotype_summary)
export(redeemR)
export(redeemR.read)
export(redeemR.read.multiple.trim)
export(redeemR.read.trim)
export(run_redeem_qc)
export(theme_cw1)
export(theme_cw2)
exportClasses(Datatoplots)
exportClasses(DistObjects)
exportClasses(TREE)
exportClasses(mitoTracing)
exportClasses(redeemR)
exportMethods(AddDatatoplot_clustering)
exportMethods(AddDist)
exportMethods(AddDist_legacy)
exportMethods(AddTree)
exportMethods(Add_AssignVariant)
exportMethods(Add_DepthMatrix)
exportMethods(Add_tree_cut)
exportMethods(Make_matrix)
exportMethods(Make_tree)
exportMethods(Make_tree_legacy)
exportMethods(SeuratLSIClustering)
exportMethods(show)
import(Matrix)
import(RColorBrewer)
import(Seurat)
import(ape)
import(doMC)
import(doParallel)
import(dplyr)
import(foreach)
import(ggExtra)
import(ggnewscale)
import(ggplot2)
import(ggtreeExtra)
import(phangorn)
import(phytools)
import(qvalue)
import(reshape2)
import(tibble)
import(tidytree)
importFrom(ggtree,ggtree)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,get.adjacency)
importFrom(igraph,graph.edgelist)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(pryr,mem_used)