API for campbio/BAGEL
Novel Mutational Signature Analysis
| Global functions | |
|---|---|
| %>% | Man page |
| .addSmallLegend | Source code |
| .check_headers | Source code |
| .check_variant_genome | Source code |
| .check_variant_ref_in_genome | Source code |
| .count1 | Source code |
| .count2_del | Source code |
| .count2_ins | Source code |
| .count_repeat | Source code |
| .create_count_table | Source code |
| .extract_count_table | Source code |
| .get_indel_motifs | Source code |
| .gg_color_hue | Source code |
| .gg_default_theme | Source code |
| .micro_left | Source code |
| .micro_right | Source code |
| .multi_modal_discovery | Source code |
| .required_bagel_headers | Source code |
| .required_maf_headers | Source code |
| .table_exists_warning | Source code |
| Result-class | Man page |
| Result_Grid-class | Man page |
| add_flank_to_variants | Man page Source code |
| add_sample_annotations | Man page Source code |
| add_variant_type | Man page Source code |
| annotate_replication_strand | Man page Source code |
| annotate_transcript_strand | Man page Source code |
| annotate_variant_length | Man page Source code |
| annotate_variant_type | Man page Source code |
| auto_predict_grid | Man page Source code |
| auto_subset_sigs | Man page Source code |
| bagel-class | Man page |
| build_custom_table | Man page Source code |
| build_standard_table | Man page Source code |
| combine_count_tables | Source code |
| combine_predict_grid | Man page Source code |
| compare_cosmic_v2 | Man page Source code |
| compare_cosmic_v3 | Man page Source code |
| compare_results | Man page Source code |
| cosmic_v2_sigs | Man page |
| cosmic_v2_subtype_map | Man page Source code |
| cosmic_v3_dbs_sigs | Man page |
| cosmic_v3_indel_sigs | Man page |
| cosmic_v3_sbs_sigs | Man page |
| cosmic_v3_sbs_sigs_exome | Man page |
| count_table-class | Man page |
| create_bagel | Man page Source code |
| create_dbs_table | Man page Source code |
| create_indel_table | Source code |
| create_sbs192_table | Man page Source code |
| create_sbs96_table | Man page Source code |
| create_umap | Man page Source code |
| discover_signatures | Man page Source code |
| drop_annotation | Man page Source code |
| drop_count_table | Source code |
| drop_na_variants | Source code |
| extract_count_tables | Man page Source code |
| extract_variants | Man page Source code |
| extract_variants_from_maf | Man page Source code |
| extract_variants_from_maf_file | Man page Source code |
| extract_variants_from_matrix | Man page Source code |
| extract_variants_from_vcf | Man page Source code |
| extract_variants_from_vcf_file | Man page Source code |
| generate_result_grid | Man page Source code |
| get_sample_annotations | Man page Source code |
| get_sample_names | Man page Source code |
| get_variants | Man page Source code |
| init_sample_annotations | Man page Source code |
| jsd | Man page Source code |
| kld | Source code |
| lda_posterior | Source code |
| name_signatures | Man page Source code |
| plot_exposures | Man page Source code |
| plot_exposures_by_annotation | Man page Source code |
| plot_full | Man page Source code |
| plot_sample_counts | Man page Source code |
| plot_sample_reconstruction_error | Man page Source code |
| plot_signatures | Man page Source code |
| plot_umap | Man page Source code |
| plot_umap_sigs | Man page Source code |
| predict_decompTumor2Sig | Source code |
| predict_exposure | Man page Source code |
| rc | Man page Source code |
| reconstruct_sample | Source code |
| rep_range | Man page |
| select_genome | Man page Source code |
| set_sample_annotations | Man page Source code |
| sig_compare | Source code |
| subset_bagel_by_annotation | Man page Source code |
| subset_bagel_by_counts | Man page Source code |
| subset_count_tables | Source code |
| subset_variant_by_type | Man page Source code |
| subset_variants_by_samples | Man page Source code |
| table_96 | Man page Source code |
| whichSignatures | Source code |
