├── .Rbuildignore ├── .circleci └── config.yml ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── docker.yaml │ └── pkgdown.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── class.R ├── data.R ├── diagnostics.R ├── genotyping.R ├── hmm.R ├── main.R ├── trees.R ├── utils.R ├── vis.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── data-raw └── prep_data.R ├── data ├── acen_hg19.rda ├── acen_hg38.rda ├── annot_ref.rda ├── bulk_example.rda ├── chrom_sizes_hg19.rda ├── chrom_sizes_hg38.rda ├── count_mat_example.rda ├── count_mat_ref.rda ├── df_allele_example.rda ├── gaps_hg19.rda ├── gaps_hg38.rda ├── gexp_roll_example.rda ├── gtf_hg19.rda ├── gtf_hg38.rda ├── gtf_mm10.rda ├── hc_example.rda ├── joint_post_example.rda ├── mut_graph_example.rda ├── phylogeny_example.rda ├── pre_likelihood_hmm.rda ├── ref_hca.rda ├── ref_hca_counts.rda ├── segs_example.rda └── vcf_meta.rda ├── docker └── Dockerfile ├── docs ├── 404.html ├── LICENSE-text.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── descriptions.html │ ├── hmm.html │ ├── hmm_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── index.html │ ├── mouse.html │ ├── numbat-multiome.html │ ├── numbat.html │ ├── results.html │ ├── results_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── spatial-rna.html │ └── test2.html ├── authors.html ├── deps │ ├── bootstrap-5.1.0 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.2.2 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.4.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Modes.html │ ├── Numbat.html │ ├── Rplot001.png │ ├── acen_hg19.html │ ├── acen_hg38.html │ ├── aggregate_counts.html │ ├── analyze_bulk.html │ ├── annot_cm.html │ ├── annot_consensus.html │ ├── annot_haplo_segs.html │ ├── annot_ref.html │ ├── annot_segs.html │ ├── annot_superclones.html │ ├── annot_theta_mle.html │ ├── annot_theta_roll.html │ ├── annotate_genes.html │ ├── approx_phi_post.html │ ├── approx_theta_post.html │ ├── binary_entropy.html │ ├── bulk_example.html │ ├── calc_allele_LLR.html │ ├── calc_allele_lik.html │ ├── calc_cluster_dist.html │ ├── calc_exp_LLR.html │ ├── calc_phi_mle_lnpois.html │ ├── calc_trans_mat.html │ ├── check_allele_df.html │ ├── check_contam.html │ ├── check_exp_noise.html │ ├── check_exp_ref.html │ ├── check_gtf_input.html │ ├── check_matrix.html │ ├── check_segs_fix.html │ ├── check_segs_loh.html │ ├── choose_ref_cor.html │ ├── chrom_sizes_hg19.html │ ├── chrom_sizes_hg38.html │ ├── classify_alleles.html │ ├── cnv_heatmap.html │ ├── combine_bulk.html │ ├── compute_posterior.html │ ├── contract_nodes.html │ ├── count_mat_example.html │ ├── count_mat_ref.html │ ├── dbbinom.html │ ├── detect_clonal_loh.html │ ├── df_allele_example.html │ ├── dpoilog.html │ ├── exp_hclust.html │ ├── expand_states.html │ ├── fill_neu_segs.html │ ├── filter_genes.html │ ├── find_common_diploid.html │ ├── fit_bbinom.html │ ├── fit_gamma.html │ ├── fit_gpois.html │ ├── fit_lnpois.html │ ├── fit_ref_sse.html │ ├── fit_snp_rate.html │ ├── forward_back_allele.html │ ├── gaps_hg19.html │ ├── gaps_hg38.html │ ├── generate_postfix.html │ ├── genotype.html │ ├── get_allele_bulk.html │ ├── get_allele_hmm.html │ ├── get_allele_post.html │ ├── get_bulk.html │ ├── get_clone_post.html │ ├── get_exp_bulk.html │ ├── get_exp_likelihoods.html │ ├── get_exp_post.html │ ├── get_exp_sc.html │ ├── get_gtree.html │ ├── get_haplotype_post.html │ ├── get_inter_cm.html │ ├── get_internal_nodes.html │ ├── get_joint_post.html │ ├── get_lambdas_bar.html │ ├── get_move_cost.html │ ├── get_move_opt.html │ ├── get_mut_tree.html │ ├── get_nodes_celltree.html │ ├── get_ordered_tips.html │ ├── get_segs_consensus.html │ ├── get_segs_neu.html │ ├── get_snps.html │ ├── get_trans_probs.html │ ├── get_tree_post.html │ ├── gexp_roll_example.html │ ├── gtf_hg19.html │ ├── gtf_hg38.html │ ├── gtf_mm10.html │ ├── hc_example.html │ ├── index.html │ ├── joint_post_example.html │ ├── l_bbinom.html │ ├── l_gpois.html │ ├── l_lnpois.html │ ├── l_s_v.html │ ├── label_edges.html │ ├── label_genotype.html │ ├── ladderize.html │ ├── likelihood_joint.html │ ├── log_mem.html │ ├── log_message.html │ ├── make_group_bulks.html │ ├── mark_tumor_lineage.html │ ├── mut_graph_example.html │ ├── mut_to_tree.html │ ├── nni.html │ ├── nnin.html │ ├── perform_nni.html │ ├── phi_hat_roll.html │ ├── phi_hat_seg.html │ ├── phylogeny_example.html │ ├── plot_bulks.html │ ├── plot_consensus.html │ ├── plot_exp_roll.html │ ├── plot_mut_history.html │ ├── plot_phylo_heatmap.html │ ├── plot_psbulk.html │ ├── plot_sc_tree.html │ ├── pnorm.range.log.html │ ├── pre_likelihood_hmm.html │ ├── preprocess_allele.html │ ├── ref_hca.html │ ├── ref_hca_counts.html │ ├── relevel_chrom.html │ ├── resolve_cnvs.html │ ├── retest_bulks.html │ ├── retest_cnv.html │ ├── return_missing_columns.html │ ├── run_allele_hmm.html │ ├── run_group_hmms.html │ ├── run_joint_hmm.html │ ├── run_numbat.html │ ├── score_mut.html │ ├── score_mut_helper.html │ ├── score_tree.html │ ├── segs_example.html │ ├── simes_p.html │ ├── simplify_history.html │ ├── smooth_expression.html │ ├── smooth_segs.html │ ├── switch_prob_cm.html │ ├── t.test.pval.html │ ├── t_test_pval.html │ ├── test_multi_allelic.html │ ├── theta_hat_roll.html │ ├── theta_hat_seg.html │ ├── to_phylo.html │ ├── transfer_links.html │ ├── upgma.html │ ├── vcf_meta.html │ ├── viterbi_allele.html │ ├── viterbi_joint.html │ └── viterbi_loh.html ├── search.json └── sitemap.xml ├── inst ├── CITATION ├── bin │ ├── get_binned_atac.R │ ├── get_binned_rna.R │ ├── get_gene_binned_intersections.R │ ├── input_prep.R │ ├── pileup_and_phase.R │ └── run_numbat_multiome.R └── extdata │ ├── gtf_hg38_bin.csv │ └── var220kb.rds ├── logo.png ├── man ├── Modes.Rd ├── Numbat.Rd ├── acen_hg19.Rd ├── acen_hg38.Rd ├── aggregate_counts.Rd ├── analyze_bulk.Rd ├── annot_consensus.Rd ├── annot_haplo_segs.Rd ├── annot_ref.Rd ├── annot_segs.Rd ├── annot_theta_mle.Rd ├── annot_theta_roll.Rd ├── annotate_genes.Rd ├── approx_phi_post.Rd ├── approx_theta_post.Rd ├── binary_entropy.Rd ├── bulk_example.Rd ├── calc_allele_LLR.Rd ├── calc_allele_lik.Rd ├── calc_cluster_dist.Rd ├── calc_exp_LLR.Rd ├── calc_phi_mle_lnpois.Rd ├── check_allele_df.Rd ├── check_contam.Rd ├── check_exp_noise.Rd ├── check_exp_ref.Rd ├── check_gtf_input.Rd ├── check_matrix.Rd ├── check_segs_fix.Rd ├── check_segs_loh.Rd ├── choose_ref_cor.Rd ├── chrom_sizes_hg19.Rd ├── chrom_sizes_hg38.Rd ├── classify_alleles.Rd ├── cnv_heatmap.Rd ├── combine_bulk.Rd ├── compute_posterior.Rd ├── contract_nodes.Rd ├── count_mat_example.Rd ├── count_mat_ref.Rd ├── detect_clonal_loh.Rd ├── df_allele_example.Rd ├── exp_hclust.Rd ├── expand_states.Rd ├── fill_neu_segs.Rd ├── filter_genes.Rd ├── find_common_diploid.Rd ├── fit_bbinom.Rd ├── fit_gamma.Rd ├── fit_lnpois.Rd ├── fit_ref_sse.Rd ├── fit_snp_rate.Rd ├── gaps_hg19.Rd ├── gaps_hg38.Rd ├── generate_postfix.Rd ├── genotype.Rd ├── get_allele_bulk.Rd ├── get_allele_hmm.Rd ├── get_allele_post.Rd ├── get_bulk.Rd ├── get_clone_post.Rd ├── get_exp_bulk.Rd ├── get_exp_likelihoods.Rd ├── get_exp_post.Rd ├── get_exp_sc.Rd ├── get_gtree.Rd ├── get_haplotype_post.Rd ├── get_inter_cm.Rd ├── get_internal_nodes.Rd ├── get_joint_post.Rd ├── get_lambdas_bar.Rd ├── get_move_cost.Rd ├── get_move_opt.Rd ├── get_nodes_celltree.Rd ├── get_ordered_tips.Rd ├── get_segs_consensus.Rd ├── get_segs_neu.Rd ├── get_snps.Rd ├── get_tree_post.Rd ├── gexp_roll_example.Rd ├── gtf_hg19.Rd ├── gtf_hg38.Rd ├── gtf_mm10.Rd ├── hc_example.Rd ├── joint_post_example.Rd ├── label_edges.Rd ├── label_genotype.Rd ├── log_mem.Rd ├── log_message.Rd ├── make_group_bulks.Rd ├── mark_tumor_lineage.Rd ├── mut_graph_example.Rd ├── phi_hat_roll.Rd ├── phi_hat_seg.Rd ├── phylogeny_example.Rd ├── plot_bulks.Rd ├── plot_consensus.Rd ├── plot_exp_roll.Rd ├── plot_mut_history.Rd ├── plot_phylo_heatmap.Rd ├── plot_psbulk.Rd ├── plot_sc_tree.Rd ├── pnorm.range.log.Rd ├── pre_likelihood_hmm.Rd ├── preprocess_allele.Rd ├── ref_hca.Rd ├── ref_hca_counts.Rd ├── relevel_chrom.Rd ├── resolve_cnvs.Rd ├── retest_bulks.Rd ├── retest_cnv.Rd ├── return_missing_columns.Rd ├── run_group_hmms.Rd ├── run_numbat.Rd ├── segs_example.Rd ├── simes_p.Rd ├── simplify_history.Rd ├── smooth_expression.Rd ├── smooth_segs.Rd ├── switch_prob_cm.Rd ├── t_test_pval.Rd ├── test_multi_allelic.Rd ├── theta_hat_roll.Rd ├── theta_hat_seg.Rd ├── transfer_links.Rd ├── upgma.Rd ├── vcf_meta.Rd └── viterbi_loh.Rd ├── numbat.png ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── misc.cpp ├── tests ├── testthat.R └── testthat │ └── test_functions.R └── vignettes ├── descriptions.Rmd ├── mouse.Rmd ├── numbat-multiome.Rmd ├── numbat.Rmd ├── results.Rmd └── spatial-rna.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 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