API for whtns/numbat
Haplotype-Aware CNV Analysis from scRNA-Seq
| Global functions | |
|---|---|
| .onLoad | Source code |
| CgetQ | Source code |
| Modes | Man page |
| Numbat | Man page |
| acen_hg19 | Man page |
| acen_hg38 | Man page |
| aggregate_counts | Man page Source code |
| allChildrenCPP | Source code |
| analyze_bulk | Man page |
| annot_bar | Source code |
| annot_consensus | Man page |
| annot_haplo_segs | Man page |
| annot_ref | Man page |
| annot_segs | Man page |
| annot_superclones | Man page |
| annot_theta_roll | Man page |
| approx_phi_post | Man page |
| approx_theta_post | Man page |
| binary_entropy | Man page |
| bulk_example | Man page |
| calc_allele_LLR | Man page |
| calc_allele_lik | Man page |
| calc_cluster_dist | Man page |
| calc_exp_LLR | Man page |
| calc_phi_mle_lnpois | Man page |
| calc_trans_mat | Man page |
| check_allele_df | Man page |
| check_exp_ref | Man page |
| check_fread_works | Source code |
| check_matrix | Man page |
| check_rds_works | Source code |
| choose_ref_cor | Man page Source code |
| chrom_sizes_hg19 | Man page |
| chrom_sizes_hg38 | Man page |
| classify_alleles | Man page |
| cnv_heatmap | Man page Source code |
| combine_bulk | Man page Source code |
| compute_posterior | Man page |
| contract_nodes | Man page |
| count_mat_example | Man page |
| count_mat_ref | Man page |
| cpp_dgpois | Source code |
| cppdbbinom | Source code |
| dbbinom | Man page Source code |
| detect_clonal_loh | Man page |
| df_allele_example | Man page |
| dpoilog | Man page Source code |
| exp_hclust | Man page Source code |
| expand_states | Man page |
| fill_neu_segs | Man page Source code |
| filter_genes | Man page Source code |
| find_common_diploid | Man page |
| fit_bbinom | Man page |
| fit_gamma | Man page |
| fit_gpois | Man page |
| fit_lnpois | Man page |
| fit_lnpois_cpp | Source code |
| fit_ref_sse | Man page |
| forward_back_allele | Man page Source code |
| forward_backward_compute | Source code |
| gaps_hg19 | Man page |
| gaps_hg38 | Man page |
| genotype | Man page Source code |
| get_allele_bulk | Man page Source code |
| get_allele_hmm | Man page Source code |
| get_allele_post | Man page |
| get_bulk | Man page |
| get_clone_post | Man page Source code |
| get_exp_bulk | Man page Source code |
| get_exp_likelihoods | Man page |
| get_exp_post | Man page |
| get_exp_sc | Man page |
| get_haplotype_post | Man page |
| get_internal_nodes | Man page |
| get_joint_post | Man page |
| get_lambdas_bar | Man page Source code |
| get_move_cost | Man page |
| get_move_opt | Man page |
| get_mut_tree | Man page Source code |
| get_nodes_celltree | Man page |
| get_segs_consensus | Man page Source code |
| get_segs_neu | Man page |
| get_snps | Man page Source code |
| get_trans_probs | Man page |
| get_tree_post | Man page Source code |
| gexp_roll_example | Man page |
| gtf_hg19 | Man page |
| gtf_hg38 | Man page |
| hc_example | Man page |
| joint_post_example | Man page |
| l_bbinom | Man page |
| l_gpois | Man page |
| l_lnpois | Man page |
| l_lnpois_cpp | Source code |
| l_s_v | Man page Source code |
| label_edges | Man page Source code |
| label_genotype | Man page Source code |
| ladderize | Man page Source code |
| likelihood_allele | Source code |
| likelihood_compute | Source code |
| logSumExp | Source code |
| make_group_bulks | Man page Source code |
| make_vcf_chr | Source code |
| mark_tumor_lineage | Man page Source code |
| mut_graph_example | Man page |
| mut_to_tree | Man page Source code |
| nni | Man page Source code |
| nni_cpp | Source code |
| nni_cpp_parallel | Source code |
| nnin | Man page Source code |
| nnin_cpp | Source code |
| node_depth | Source code |
| oob_squish | Source code |
| perform_nni | Man page Source code |
| phi_hat_roll | Man page |
| phi_hat_seg | Man page |
| phylogeny_example | Man page |
| plot_bulks | Man page Source code |
| plot_clone_profile | Source code |
| plot_consensus | Man page Source code |
| plot_exp_post | Source code |
| plot_exp_roll | Man page Source code |
| plot_mut_history | Man page Source code |
| plot_phylo_heatmap | Man page Source code |
| plot_psbulk | Man page Source code |
| plot_sc_tree | Man page Source code |
| pnorm.range.log | Man page |
| poilog1 | Source code |
| pre_likelihood_hmm | Man page |
| preprocess_allele | Man page Source code |
| read_file | Source code |
| read_hc_rds | Source code |
| ref_hca | Man page |
| ref_hca_counts | Man page |
| relevel_chrom | Source code |
| reorderRcpp | Source code |
| reorder_rows | Source code |
| resolve_cnvs | Man page Source code |
| retest_bulks | Man page |
| retest_cnv | Man page |
| return_missing_columns | Source code |
| roman2int_internal | Source code |
| run_allele_hmm | Man page Source code |
| run_group_hmms | Man page Source code |
| run_joint_hmm | Man page Source code |
| run_numbat | Man page Source code |
| scale_counts | Source code |
| score_mut | Man page |
| score_mut_helper | Man page |
| score_nni_parallel | Source code |
| score_tree | Man page Source code |
| score_tree_cpp | Source code |
| segs_equal | Source code |
| segs_example | Man page |
| show_phasing | Source code |
| simes_p | Man page |
| simplify_history | Man page |
| smooth_expression | Man page Source code |
| smooth_segs | Man page |
| subtrees_equal | Source code |
| switch_prob_cm | Man page |
| test_multi_allelic | Man page |
| theta_hat_roll | Man page |
| theta_hat_seg | Man page |
| to_phylo | Man page Source code |
| transfer_links | Man page Source code |
| upgma | Man page Source code |
| vcf_meta | Man page |
| viterbi_allele | Man page Source code |
| viterbi_compute | Source code |
| viterbi_joint | Man page |
| viterbi_loh | Man page |
