API for ShixiangWang/sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
| Global functions | |
|---|---|
| %>% | Man page |
| .collapse_segTab | Source code |
| .data | Man page |
| .env | Man page |
| .onAttach | Source code |
| .onLoad | Source code |
| := | Man page |
| BayesNMF.L1.KL.fixed_W.Z | Source code |
| BayesNMF.L1.KL.fixed_W.Z.sample | Source code |
| BayesNMF.L1KL | Source code |
| BayesNMF.L1W.L2H | Source code |
| BayesNMF.L2KL | Source code |
| CN.features | Man page |
| CopyNumber | Man page |
| CopyNumber-class | Man page |
| FrobeniusNorm | Source code |
| IntersectSize | Source code |
| MAF | Man page |
| MAF-class | Man page |
| `%:::%` | Source code |
| add_h_arrow | Man page Source code |
| add_labels | Man page Source code |
| as_label | Man page |
| as_name | Man page |
| assert_class | Source code |
| bootstrap_p_value | Source code |
| bp | Man page |
| bp_attribute_activity | Man page |
| bp_cluster_iter_list | Man page |
| bp_extract_signatures | Man page Source code |
| bp_extract_signatures_iter | Man page |
| bp_get_clustered_sigs | Man page |
| bp_get_rank_score | Man page |
| bp_get_sig_obj | Man page |
| bp_get_stats | Man page |
| bp_show_survey | Man page |
| bp_show_survey2 | Man page |
| build_chrom_coordinate | Source code |
| build_opps_matrix | Source code |
| call_component | Source code |
| call_component_sv | Source code |
| centromeres.T2T | Man page |
| centromeres.hg19 | Man page |
| centromeres.hg38 | Man page |
| centromeres.mm10 | Man page |
| centromeres.mm9 | Man page |
| check_nmf_matrix | Source code |
| chromsize.T2T | Man page |
| chromsize.hg19 | Man page |
| chromsize.hg38 | Man page |
| chromsize.mm10 | Man page |
| chromsize.mm9 | Man page |
| chunk2 | Source code |
| cmp_one | Source code |
| col2hex | Source code |
| collapse_hyper_records | Source code |
| cosine | Man page Source code |
| cosineMatrix | Source code |
| cosineVector | Source code |
| count_components | Source code |
| count_components_wrapper | Source code |
| cytobands.T2T | Man page |
| cytobands.hg19 | Man page |
| cytobands.hg38 | Man page |
| cytobands.mm10 | Man page |
| cytobands.mm9 | Man page |
| decompose_NNLS | Source code |
| decompose_QP | Source code |
| decompose_SA | Source code |
| deploy_sigflow | Source code |
| enquo | Man page |
| enquos | Man page |
| enrich_component_strand_bias | Man page Source code |
| enrich_one | Source code |
| expr | Man page |
| file_name | Source code |
| find_enriched_signature | Source code |
| generate_matrix_SBS | Source code |
| getAB | Source code |
| getBP10MB_v2 | Source code |
| getBPnum | Source code |
| getBoChr | Source code |
| getCN | Source code |
| getCN_v2 | Source code |
| getCS | Source code |
| getCentromereDistCounts | Source code |
| getChangepointCN | Source code |
| getClustered | Source code |
| getDists | Source code |
| getLOH | Source code |
| getNC50 | Source code |
| getNChrV | Source code |
| getOscilation | Source code |
| getRearrSize | Source code |
| getSegsize | Source code |
| getSegsize_v2 | Source code |
| getType | Source code |
| get_3d_array_stats | Source code |
| get_Aneuploidy_score | Man page Source code |
| get_ArmLocation | Source code |
| get_LengthFraction | Source code |
| get_adj_p | Man page Source code |
| get_bayesian_result | Man page Source code |
| get_cn_freq_table | Man page Source code |
| get_cn_ploidy | Man page Source code |
| get_cnlist | Source code |
| get_cnsummary_sample | Source code |
| get_components_mutex | Source code |
| get_components_sv | Source code |
| get_expo_corr_stat | Source code |
| get_feature_components | Source code |
| get_features_mutex | Source code |
| get_features_sv | Source code |
| get_features_wang | Source code |
| get_genome_annotation | Man page Source code |
| get_group_comparison | Man page Source code |
| get_groups | Man page Source code |
| get_intersect_size | Man page Source code |
| get_matrix_mutex | Source code |
| get_matrix_sv | Source code |
| get_pLOH_score | Man page Source code |
| get_segsize_order | Source code |
| get_shannon_diversity_index | Man page Source code |
| get_sig_cancer_type_index | Man page Source code |
| get_sig_db | Man page Source code |
| get_sig_exposure | Man page Source code |
| get_sig_feature_association | Man page Source code |
| get_sig_rec_similarity | Man page Source code |
| get_sig_similarity | Man page Source code |
| get_similarity_stats | Source code |
| get_stat_samps | Source code |
| get_stat_sigs | Source code |
| get_svclass | Source code |
| get_svlist | Source code |
| get_tidy_association | Man page Source code |
| get_timestamp | Source code |
| group_enrichment | Man page Source code |
| group_enrichment2 | Man page Source code |
| handle_hyper_mutation | Man page Source code |
| handle_sex | Source code |
| hcbottom | Source code |
| hello | Man page Source code |
| helper_create_chunks | Source code |
| helper_create_colormap | Source code |
| helper_join_segments2 | Source code |
| helper_normalize_by_feature | Source code |
| helper_scale_nmf_matrix | Source code |
| helper_sort_signature | Source code |
| human_trinuc_freqs | Source code |
| is.wholenumber | Source code |
| isValidAndUnreserved | Source code |
| kmvar | Source code |
| mem_used | Source code |
| mutate_cond | Source code |
| my.t.test.p.value | Source code |
| nnit | Source code |
| node_size | Source code |
| norm2rg | Source code |
| normalize_solution | Source code |
| output_bootstrap | Man page Source code |
| output_fit | Man page Source code |
| output_sig | Man page Source code |
| output_tally | Man page Source code |
| pairwise.fisher.test | Source code |
| parse_cosmic | Source code |
| plot_cn_circos | Source code |
| plot_cn_circos_density | Source code |
| plot_cn_profile | Source code |
| plot_cn_summary | Source code |
| plot_enrichment_simple | Source code |
| print.bytes | Source code |
| process_solution | Source code |
| query_remote_data | Source code |
| quote_opt | Source code |
| read_ascat_cn | Source code |
| read_ascat_cn_list | Source code |
| read_copynumber | Man page Source code |
| read_copynumber_ascat | Man page Source code |
| read_copynumber_seqz | Man page Source code |
| read_maf | Man page Source code |
| read_maf_minimal | Man page Source code |
| read_sigprofiler_solution | Source code |
| read_sv_as_rs | Man page Source code |
| read_vcf | Man page Source code |
| read_xena_variants | Man page Source code |
| report_bootstrap_p_value | Man page Source code |
| return_expo | Source code |
| rgb2hex | Source code |
| same_size_clustering | Man page Source code |
| scoring | Man page Source code |
| scoring_Chromoth | Source code |
| scoring_MACN | Source code |
| scoring_TD | Source code |
| send_elapsed_time | Source code |
| send_error | Source code |
| send_info | Source code |
| send_stop | Source code |
| send_success | Source code |
| send_warning | Source code |
| set_future_strategy | Source code |
| shifter | Source code |
| show_bytes | Source code |
| show_catalogue | Man page Source code |
| show_cn_circos | Man page Source code |
| show_cn_components | Man page Source code |
| show_cn_distribution | Man page Source code |
| show_cn_features | Man page Source code |
| show_cn_freq_circos | Man page Source code |
| show_cn_group_profile | Man page Source code |
| show_cn_profile | Man page Source code |
| show_cor | Man page Source code |
| show_cosmic | Man page Source code |
| show_cosmic_sig_profile | Man page Source code |
| show_group_comparison | Man page Source code |
| show_group_distribution | Man page Source code |
| show_group_enrichment | Man page Source code |
| show_group_mapping | Man page Source code |
| show_groups | Man page Source code |
| show_sig_bootstrap | Man page |
| show_sig_bootstrap_error | Man page Source code |
| show_sig_bootstrap_exposure | Man page Source code |
| show_sig_bootstrap_stability | Man page Source code |
| show_sig_consensusmap | Man page Source code |
| show_sig_exposure | Man page Source code |
| show_sig_feature_corrplot | Man page Source code |
| show_sig_fit | Man page Source code |
| show_sig_number_survey | Man page Source code |
| show_sig_number_survey2 | Man page Source code |
| show_sig_profile | Man page Source code |
| show_sig_profile_heatmap | Man page Source code |
| show_sig_profile_loop | Man page Source code |
| sig_attrs | Man page Source code |
| sig_auto_extract | Man page Source code |
| sig_convert | Man page Source code |
| sig_estimate | Man page Source code |
| sig_exposure | Man page Source code |
| sig_extract | Man page Source code |
| sig_fit | Man page Source code |
| sig_fit_bootstrap | Man page Source code |
| sig_fit_bootstrap_batch | Man page Source code |
| sig_modify_names | Man page Source code |
| sig_names | Man page Source code |
| sig_number | Man page Source code |
| sig_operation | Man page |
| sig_signature | Man page Source code |
| sig_tally | Man page Source code |
| sig_tally.CopyNumber | Man page Source code |
| sig_tally.MAF | Man page Source code |
| sig_tally.RS | Man page Source code |
| sig_unify_extract | Man page Source code |
| sigminer | Man page |
| sigminer-package | Man page |
| sigprofiler | Man page |
| sigprofiler_extract | Man page Source code |
| sigprofiler_import | Man page Source code |
| sigprofiler_reorder | Man page Source code |
| simulate_catalogue | Man page Source code |
| simulate_catalogue_matrix | Man page Source code |
| simulate_signature | Man page Source code |
| simulated_catalogs | Man page |
| simulation | Man page |
| split_seq | Source code |
| subset.CopyNumber | Man page Source code |
| sym | Man page |
| syms | Man page |
| tbl_one | Source code |
| tf_signature | Source code |
| tidyeval | Man page |
| transcript.T2T | Man page |
| transcript.hg19 | Man page |
| transcript.hg38 | Man page |
| transcript.mm10 | Man page |
| transcript.mm9 | Man page |
| transform_seg_table | Man page Source code |
| use_color_style | Man page Source code |
| validate_segTab | Source code |
