API for CuppenResearch/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes
| Global functions | |
|---|---|
| .calc_chrom_ends | Source code |
| .calculate_mismatches | Source code |
| .check_chroms | Source code |
| .check_no_indels | Source code |
| .check_no_indels_gr | Source code |
| .check_no_multi_alts | Source code |
| .check_no_multi_alts_gr | Source code |
| .check_no_substitutions | Source code |
| .check_no_substitutions_gr | Source code |
| .count_dbs_contexts_gr | Source code |
| .count_indel_contexts_gr | Source code |
| .count_mbs_contexts_gr | Source code |
| .create_dummy_limits | Source code |
| .create_profile_comparison | Source code |
| .filter_seqlevels | Source code |
| .find_potential_splice_site_muts | Source code |
| .find_potential_splice_site_muts_strand | Source code |
| .find_substitution | Source code |
| .get_1bp_dels | Source code |
| .get_1bp_ins | Source code |
| .get_alt | Source code |
| .get_big_dels | Source code |
| .get_big_ins | Source code |
| .get_cds_ranges | Source code |
| .get_cds_sequences | Source code |
| .get_cos_sim_ori_vs_rec | Source code |
| .get_dbs_context_gr | Source code |
| .get_extended_sequence | Source code |
| .get_indel_context_gr | Source code |
| .get_mut_type_gr | Source code |
| .get_ref | Source code |
| .get_ref_codons | Source code |
| .get_sig_star | Source code |
| .get_splice_genelocs | Source code |
| .get_splice_single_genelocs | Source code |
| .get_splice_site_ranges | Source code |
| .get_splice_site_ranges_gr | Source code |
| .get_splice_site_sequences | Source code |
| .get_x_axis_breaks | Source code |
| .indel_count_n_repeats | Source code |
| .indel_get_n_repeats | Source code |
| .indel_get_n_repeats_left | Source code |
| .indel_get_n_repeats_right | Source code |
| .intersect_with_region | Source code |
| .is_na | Source code |
| .mutate_codon | Source code |
| .not_gr | Source code |
| .not_gr_or_grl | Source code |
| .plot_lesion_segregation_gg | Source code |
| .plot_regional_similarity_gg | Source code |
| .plot_sim_decay | Source code |
| .potential_splice_site_damage | Source code |
| .read_single_vcf_as_grange | Source code |
| .remove_indels | Source code |
| .remove_indels_gr | Source code |
| .remove_multi_alts_variants | Source code |
| .remove_multi_alts_variants_gr | Source code |
| .remove_substitutions | Source code |
| .remove_substitutions_gr | Source code |
| .resample_mut_mat | Source code |
| .river_create_context_matrix | Source code |
| .river_create_lodes | Source code |
| .river_plot_river | Source code |
| .set_large_indels_as_5plus | Source code |
| .single_context_damage_analysis | Source code |
| .single_context_damage_analysis_strand | Source code |
| .split_mbs_gr | Source code |
| .strict_refit_backwards_selection_sample | Source code |
| .strict_refit_best_subset_selection_sample | Source code |
| .strict_refit_best_subset_selection_sample_n | Source code |
| .strict_refit_best_subset_selection_single_set | Source code |
| .subsample_granges | Source code |
| MutationalPatterns | Man page |
| MutationalPatterns-package | Man page |
| bin_mutation_density | Man page Source code |
| binomial_test | Man page Source code |
| calculate_lesion_segregation | Man page Source code |
| cluster_signatures | Man page Source code |
| context_potential_damage_analysis | Man page Source code |
| convert_sigs_to_ref | Man page Source code |
| cos_sim | Man page Source code |
| cos_sim_matrix | Man page Source code |
| count_dbs_contexts | Man page Source code |
| count_indel_contexts | Man page Source code |
| count_mbs_contexts | Man page Source code |
| determine_regional_similarity | Man page Source code |
| enrichment_depletion_test | Man page Source code |
| explained_by_signatures | Man page |
| extract_signatures | Man page Source code |
| fit_to_signatures | Man page Source code |
| fit_to_signatures_bootstrapped | Man page Source code |
| fit_to_signatures_strict | Man page Source code |
| genomic_distribution | Man page Source code |
| get_dbs_context | Man page Source code |
| get_indel_context | Man page Source code |
| get_known_signatures | Man page Source code |
| get_mut_type | Man page Source code |
| get_sim_tb | Man page |
| get_sim_tb,region_cossim-method | Man page |
| lengthen_mut_matrix | Man page Source code |
| merge_signatures | Man page Source code |
| mut_192_occurrences | Man page Source code |
| mut_96_occurrences | Man page Source code |
| mut_context | Man page Source code |
| mut_matrix | Man page Source code |
| mut_matrix_stranded | Man page Source code |
| mut_strand | Man page Source code |
| mut_type | Man page Source code |
| mut_type_occurrences | Man page Source code |
| mutation_context | Man page |
| mutation_types | Man page |
| mutations_from_vcf | Man page Source code |
| plot_192_profile | Man page Source code |
| plot_96_profile | Man page Source code |
| plot_bootstrapped_contribution | Man page Source code |
| plot_compare_dbs | Man page Source code |
| plot_compare_indels | Man page Source code |
| plot_compare_mbs | Man page Source code |
| plot_compare_profiles | Man page Source code |
| plot_contribution | Man page Source code |
| plot_contribution_heatmap | Man page Source code |
| plot_correlation_bootstrap | Man page Source code |
| plot_cosine_heatmap | Man page Source code |
| plot_dbs_contexts | Man page Source code |
| plot_enrichment_depletion | Man page Source code |
| plot_indel_contexts | Man page Source code |
| plot_lesion_segregation | Man page Source code |
| plot_main_dbs_contexts | Man page Source code |
| plot_main_indel_contexts | Man page Source code |
| plot_mbs_contexts | Man page Source code |
| plot_original_vs_reconstructed | Man page Source code |
| plot_profile_heatmap | Man page Source code |
| plot_profile_region | Man page Source code |
| plot_rainfall | Man page Source code |
| plot_regional_similarity | Man page Source code |
| plot_river | Man page Source code |
| plot_signature_strand_bias | Man page Source code |
| plot_spectrum | Man page Source code |
| plot_spectrum_region | Man page Source code |
| plot_strand | Man page Source code |
| plot_strand_bias | Man page Source code |
| pool_mut_mat | Man page Source code |
| read_vcfs_as_granges | Man page Source code |
| region_cossim-class | Man page |
| rename_nmf_signatures | Man page Source code |
| show,region_cossim-method | Man page |
| signature_potential_damage_analysis | Man page Source code |
| split_muts_region | Man page Source code |
| strand_bias_test | Man page Source code |
| strand_from_vcf | Man page |
| strand_occurrences | Man page Source code |
| type_context | Man page Source code |
