Files in numbat

Haplotype-Aware CNV Analysis from scRNA-Seq

NEWS.md README.md R/RcppExports.R R/vis.R R/trees.R R/main.R R/hmm.R R/data.R R/diagnostics.R R/genotyping.R R/zzz.R R/class.R R/utils.R inst/bin/pileup_and_phase.R tests/testthat.R tests/testthat/test_functions.R man/log_message.Rd man/get_ordered_tips.Rd man/analyze_bulk.Rd man/segs_example.Rd man/binary_entropy.Rd man/df_allele_example.Rd man/count_mat_example.Rd man/get_lambdas_bar.Rd man/smooth_segs.Rd man/phi_hat_roll.Rd man/Modes.Rd man/get_nodes_celltree.Rd man/get_joint_post.Rd man/compute_posterior.Rd man/return_missing_columns.Rd man/run_numbat.Rd man/get_internal_nodes.Rd man/vcf_meta.Rd man/theta_hat_seg.Rd man/get_allele_bulk.Rd man/annot_haplo_segs.Rd man/log_mem.Rd man/calc_cluster_dist.Rd man/check_segs_loh.Rd man/annotate_genes.Rd man/check_contam.Rd man/check_allele_df.Rd man/contract_nodes.Rd man/plot_consensus.Rd man/exp_hclust.Rd man/calc_phi_mle_lnpois.Rd man/check_exp_ref.Rd man/fit_snp_rate.Rd man/gexp_roll_example.Rd man/get_exp_likelihoods.Rd man/retest_bulks.Rd man/get_allele_hmm.Rd man/test_multi_allelic.Rd man/genotype.Rd man/chrom_sizes_hg38.Rd man/transfer_links.Rd man/get_exp_sc.Rd man/label_genotype.Rd man/plot_mut_history.Rd man/gtf_hg38.Rd man/t_test_pval.Rd man/upgma.Rd man/viterbi_loh.Rd man/combine_bulk.Rd man/find_common_diploid.Rd man/gaps_hg19.Rd man/plot_bulks.Rd man/pnorm.range.log.Rd man/preprocess_allele.Rd man/get_move_cost.Rd man/fit_gamma.Rd man/retest_cnv.Rd man/plot_phylo_heatmap.Rd man/smooth_expression.Rd man/joint_post_example.Rd man/approx_phi_post.Rd man/resolve_cnvs.Rd man/fit_bbinom.Rd man/fit_ref_sse.Rd man/get_gtree.Rd man/label_edges.Rd man/phylogeny_example.Rd man/calc_allele_lik.Rd man/generate_postfix.Rd man/chrom_sizes_hg19.Rd man/choose_ref_cor.Rd man/simplify_history.Rd man/get_bulk.Rd man/get_haplotype_post.Rd man/detect_clonal_loh.Rd man/switch_prob_cm.Rd man/run_group_hmms.Rd man/get_move_opt.Rd man/get_exp_bulk.Rd man/theta_hat_roll.Rd man/annot_segs.Rd man/phi_hat_seg.Rd man/get_segs_consensus.Rd man/gaps_hg38.Rd man/get_exp_post.Rd man/classify_alleles.Rd man/filter_genes.Rd man/plot_sc_tree.Rd man/get_tree_post.Rd man/fill_neu_segs.Rd man/mut_graph_example.Rd man/pre_likelihood_hmm.Rd man/hc_example.Rd man/annot_ref.Rd man/approx_theta_post.Rd man/check_matrix.Rd man/annot_theta_mle.Rd man/ref_hca.Rd man/calc_allele_LLR.Rd man/calc_exp_LLR.Rd man/mark_tumor_lineage.Rd man/check_segs_fix.Rd man/count_mat_ref.Rd man/annot_theta_roll.Rd man/acen_hg19.Rd man/get_allele_post.Rd man/ref_hca_counts.Rd man/check_exp_noise.Rd man/get_segs_neu.Rd man/aggregate_counts.Rd man/acen_hg38.Rd man/annot_consensus.Rd man/expand_states.Rd man/get_clone_post.Rd man/Numbat.Rd man/simes_p.Rd man/gtf_mm10.Rd man/get_snps.Rd man/plot_exp_roll.Rd man/bulk_example.Rd man/relevel_chrom.Rd man/get_inter_cm.Rd man/cnv_heatmap.Rd man/make_group_bulks.Rd man/fit_lnpois.Rd man/plot_psbulk.Rd man/gtf_hg19.Rd