├── .RData ├── .Rbuildignore ├── .Rhistory ├── .gitignore ├── .ipynb_checkpoints ├── ReDeeM_R.RunningTest-checkpoint.ipynb └── scMitoTracingRunningTest-checkpoint.ipynb ├── DESCRIPTION ├── Extra.R ├── LICENSE ├── NAMESPACE ├── PythonHelper └── ComputeLikli.py ├── R ├── BuidTree.R ├── Clustering_functions.R ├── General_functions.R ├── Plot.R ├── VariantSummary.R └── log ├── README.md ├── ReDeeM_R.RunningTest.ipynb ├── activate.R ├── data-raw └── DATASET.R ├── data ├── ATACWhite.rda ├── CellPCT.rda ├── CellPCT.update.rda ├── ContextsDic.rda ├── Griffin_Signatures.rda ├── RNAWhite.rda ├── all.genes.refer.rda ├── msig.db.rda └── ref_all_long.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── articles │ ├── index.html │ └── package_intro.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── ATAC_Wrapper.html │ ├── AddDatatoplot_clustering-mitoTracing-method.html │ ├── AddDatatoplot_clustering-redeemR-method.html │ ├── AddDatatoplot_clustering.html │ ├── AddDist-mitoTracing-method.html │ ├── AddDist-redeemR-method.html │ ├── AddDist.html │ ├── AddHemSignature.html │ ├── AddTree-mitoTracing-method.html │ ├── AddTree-redeemR-method.html │ ├── AddTree.html │ ├── Add_AssignVariant-mitoTracing-method.html │ ├── Add_AssignVariant-redeemR-method.html │ ├── Add_AssignVariant.html │ ├── Add_DepthMatrix-mitoTracing-method.html │ ├── Add_DepthMatrix-redeemR-method.html │ ├── Add_DepthMatrix.html │ ├── Add_tree_cut-mitoTracing-method.html │ ├── Add_tree_cut-redeemR-method.html │ ├── Add_tree_cut.html │ ├── BinaryDist.html │ ├── CV.html │ ├── CW_mgatk.read.html │ ├── Clone_FinderMarker.html │ ├── ComputeRejectRate.html │ ├── CountVperCell.html │ ├── Create_mitoTracing.html │ ├── Create_redeemR.html │ ├── DE.gettripple.html │ ├── Datatoplots-class.html │ ├── DepthSummary.html │ ├── DistObjects-class.html │ ├── DoDE.html │ ├── FromDist2Graph.html │ ├── GEM_Wrapper.html │ ├── GTSummary.html │ ├── Get_Clonal_Variants.html │ ├── LineageBiasPlot.html │ ├── MakeAllNodes.html │ ├── MakeDF4Regress.html │ ├── MakeNN.html │ ├── Make_AnnTable.html │ ├── Make_Cells4Nodes.html │ ├── Make_matrix-mitoTracing-method.html │ ├── Make_matrix-redeemR-method.html │ ├── Make_matrix.html │ ├── Make_tree-mitoTracing-method.html │ ├── Make_tree-redeemR-method.html │ ├── Make_tree.html │ ├── MergeMtx.html │ ├── Motifenrich.binom.html │ ├── Multi_Wrapper.html │ ├── MutationProfile.bulk.html │ ├── NN2M.html │ ├── ProgenyMapping.html │ ├── ProgenyMapping_np.html │ ├── Reclustering.html │ ├── Reclustering_hm.html │ ├── Rplot001.png │ ├── Run_Lin_regression.html │ ├── Run_Lin_regression_poi.html │ ├── Runplot_scale_2.html │ ├── Runplot_scale_3.html │ ├── SeuratLSIClustering-mitoTracing-method.html │ ├── SeuratLSIClustering-redeemR-method.html │ ├── SeuratLSIClustering.html │ ├── Show_Consensus.html │ ├── Subset_MitoTracing.html │ ├── Subset_redeemR.html │ ├── TREE-class.html │ ├── Tomerge_v2.html │ ├── Translate_RNA2ATAC.html │ ├── Translate_simple_ATAC2RNA.html │ ├── Translate_simple_RNA2ATAC.html │ ├── Vfilter_v3.html │ ├── Vfilter_v4.html │ ├── add_derived_profile_info.html │ ├── df2ProfileMtx.html │ ├── get_ancestral_nodes.html │ ├── index.html │ ├── mitoTracing-class.html │ ├── plot_depth.html │ ├── plot_npSummary.html │ ├── plot_variant.html │ ├── quick_w_cosine.html │ ├── quick_w_jaccard.html │ ├── reconstruct_genotype_summary.html │ ├── redeemR-class.html │ ├── redeemR.read.html │ ├── show-mitoTracing-method.html │ ├── show-redeemR-method.html │ ├── split_profile.html │ └── str2vector.html └── sitemap.xml ├── log ├── man ├── ATAC_Wrapper.Rd ├── AddDatatoplot_clustering-redeemR-method.Rd ├── AddDatatoplot_clustering.Rd ├── AddDist-redeemR-method.Rd ├── AddDist.Rd ├── AddDist_legacy-mitoTracing-method.Rd ├── AddDist_legacy.Rd ├── AddHemSignature.Rd ├── AddTree-redeemR-method.Rd ├── AddTree.Rd ├── Add_AssignVariant-redeemR-method.Rd ├── Add_AssignVariant.Rd ├── Add_DepthMatrix-redeemR-method.Rd ├── Add_DepthMatrix.Rd ├── Add_tree_cut-redeemR-method.Rd ├── Add_tree_cut.Rd ├── AddsigTag.6.new.Rd ├── Annotate_base_change.Rd ├── BinaryDist.Rd ├── CV.Rd ├── CW_mgatk.read.Rd ├── Clone_FinderMarker.Rd ├── ComputeRejectRate.Rd ├── ComputeRejectRate_legacy.Rd ├── CountOverlap_Adj.Rd ├── CountVperCell.Rd ├── Create_mitoTracing.Rd ├── Create_redeemR.Rd ├── Create_redeemR_model.Rd ├── DE.gettripple.Rd ├── Datatoplots-class.Rd ├── DepthSummary.Rd ├── DistObjects-class.Rd ├── DoDE.Rd ├── FromDist2Graph.Rd ├── Fun.enrich_withFC.Rd ├── Fun.enrich_withFC.pvalue.Rd ├── GEM_Wrapper.Rd ├── GTSummary.Rd ├── Get_Clonal_Variants.Rd ├── Getgenenumber.Rd ├── Getpallet2.Rd ├── LineageBiasPlot.Rd ├── MakeAllNodes.Rd ├── MakeDF4Regress.Rd ├── MakeNN.Rd ├── Make_AnnTable.Rd ├── Make_Cells4Nodes.Rd ├── Make_matrix-redeemR-method.Rd ├── Make_matrix.Rd ├── Make_tree-redeemR-method.Rd ├── Make_tree.Rd ├── Make_tree_legacy-mitoTracing-method.Rd ├── Make_tree_legacy.Rd ├── MergeMtx.Rd ├── Motifenrich.binom.Rd ├── Multi_Wrapper.Rd ├── MutationProfile.bulk.Rd ├── NN2M.Rd ├── ProgenyMapping.Rd ├── ProgenyMapping_np.Rd ├── Reclustering.Rd ├── Reclustering_hm.Rd ├── Run_Lin_regression.Rd ├── Run_Lin_regression_poi.Rd ├── Runplot_scale_2.Rd ├── Runplot_scale_3.Rd ├── SeuratLSIClustering-redeemR-method.Rd ├── SeuratLSIClustering.Rd ├── Show_Consensus.Rd ├── Subset_redeemR.Rd ├── TREE-class.Rd ├── Tomerge.col.Rd ├── Tomerge_v2.Rd ├── Translate_RNA2ATAC.Rd ├── Translate_simple_ATAC2RNA.Rd ├── Translate_simple_RNA2ATAC.Rd ├── Vfilter_v3.Rd ├── Vfilter_v4.Rd ├── add_changes.Rd ├── add_derived_profile_info.Rd ├── add_freq_raw.Rd ├── add_hypermutable.Rd ├── add_raw_fragment.Rd ├── add_types.Rd ├── binomialtest.msig.enrch_deplet.Rd ├── clean_redeem.Rd ├── clean_redeem_removehot.Rd ├── convert_mitotracing_redeemR.Rd ├── convert_variant.Rd ├── df2ProfileMtx.Rd ├── get_ancestral_nodes.Rd ├── get_hype_v2.Rd ├── gsea_enrichmentheat.Rd ├── make_ks_test_df.Rd ├── make_position_df_3.4.Rd ├── make_position_df_3.5.Rd ├── mitoTracing-class.Rd ├── plot_depth.Rd ├── plot_depth_legacy.Rd ├── plot_npSummary.Rd ├── plot_variant.Rd ├── plot_variant_legacy.Rd ├── quick_w_cosine.Rd ├── quick_w_jaccard.Rd ├── reconstruct_genotype_summary.Rd ├── redeemR-class.Rd ├── redeemR.read.Rd ├── redeemR.read.multiple.trim.Rd ├── redeemR.read.trim.Rd ├── run_redeem_qc.Rd ├── show-redeemR-method.Rd ├── split_profile.Rd ├── str2vector.Rd ├── theme_cw1.Rd └── theme_cw2.Rd ├── redeemR_1.0.pdf ├── renv.lock ├── trash ├── NAMESPACE ├── NEWS.md └── REDEEM-R_0.0.0.9000.pdf └── vignettes ├── .gitignore ├── .ipynb_checkpoints ├── Get_Started-checkpoint.ipynb ├── misc_new_functions-checkpoint.ipynb └── redeem_filter2-checkpoint.ipynb ├── Get_Started.ipynb ├── misc_new_functions.ipynb ├── redeem.tmp.rds ├── redeem_filter2.ipynb └── vignettes.md /.RData: 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