R Packages that start with:
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Functions
- acen_hg19()
- acen_hg38()
- aggregate_counts()
- analyze_bulk()
- annotate_genes()
- annot_consensus()
- annot_haplo_segs()
- annot_ref()
- annot_segs()
- annot_theta_mle()
- annot_theta_roll()
- approx_phi_post()
- approx_theta_post()
- binary_entropy()
- bulk_example()
- calc_allele_lik()
- calc_allele_LLR()
- calc_cluster_dist()
- calc_exp_LLR()
- calc_phi_mle_lnpois()
- calc_trans_mat()
- check_allele_df()
- check_contam()
- check_exp_noise()
- check_exp_ref()
- check_matrix()
- check_segs_fix()
- check_segs_loh()
- choose_ref_cor()
- chrom_sizes_hg19()
- chrom_sizes_hg38()
- classify_alleles()
- cnv_heatmap()
- combine_bulk()
- compute_posterior()
- contract_nodes()
- count_mat_example()
- count_mat_ref()
- dbbinom()
- detect_clonal_loh()
- df_allele_example()
- dgpois()
- dpoilog()
- expand_states()
- exp_hclust()
- fill_neu_segs()
- filter_genes()
- find_common_diploid()
- fit_bbinom()
- fit_gamma()
- fit_gpois()
- fit_lnpois()
- fit_ref_sse()
- fit_snp_rate()
- forward_back_allele()
- gaps_hg19()
- gaps_hg38()
- generate_postfix()
- genotype()
- get_allele_bulk()
- get_allele_hmm()
- get_allele_post()
- get_bulk()
- get_clone_post()
- get_exp_bulk()
- get_exp_likelihoods()
- get_exp_post()
- get_exp_sc()
- get_gtree()
- get_haplotype_post()
- get_internal_nodes()
- get_inter_cm()
- get_joint_post()
- get_lambdas_bar()
- get_move_cost()
- get_move_opt()
- get_nodes_celltree()
- get_ordered_tips()
- get_segs_consensus()
- get_segs_neu()
- get_snps()
- get_trans_probs()
- get_tree_post()
- gexp_roll_example()
- gtf_hg19()
- gtf_hg38()
- gtf_mm10()
- hc_example()
- joint_post_example()
- label_edges()
- label_genotype()
- likelihood_allele()
- log_mem()
- log_message()
- l_bbinom()
- l_gpois()
- l_lnpois()
- make_group_bulks()
- mark_tumor_lineage()
- Modes()
- mut_graph_example()
- Numbat()
- phi_hat_roll()
- phi_hat_seg()
- phylogeny_example()
- plot_bulks()
- plot_consensus()
- plot_exp_roll()
- plot_mut_history()
- plot_phylo_heatmap()
- plot_psbulk()
- plot_sc_tree()
- pnorm.range.log()
- preprocess_allele()
- pre_likelihood_hmm()
- ref_hca()
- ref_hca_counts()
- relevel_chrom()
- resolve_cnvs()
- retest_bulks()
- retest_cnv()
- return_missing_columns()
- run_allele_hmm()
- run_group_hmms()
- run_joint_hmm()
- run_numbat()
- segs_example()
- simes_p()
- simplify_history()
- smooth_expression()
- smooth_segs()
- switch_prob_cm()
- test_multi_allelic()
- theta_hat_roll()
- theta_hat_seg()
- transfer_links()
- t_test_pval()
- upgma()
- vcf_meta()
- viterbi_allele()
- viterbi_joint()
- viterbi_loh()
R Codes
Selected R package: numbat
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