API for TRON-Bioinformatics/splice2neo
Aberrant splice junction analysis with associated mutations
| Global functions | |
|---|---|
| %>% | Man page |
| add_context_seq | Man page Source code |
| add_identified_in_RNA | Man page Source code |
| add_peptide | Man page Source code |
| add_tx | Man page Source code |
| annotate_exon_idx | Man page Source code |
| annotate_junc_in_orf | Man page Source code |
| annotate_mmsplice | Man page Source code |
| annotate_mut_effect | Man page Source code |
| annotate_truncated_cds | Man page Source code |
| bed_to_junc | Man page Source code |
| breakpoint2junc | Man page Source code |
| canonical_juncs | Man page |
| canonical_junctions | Man page Source code |
| choose_tx | Man page Source code |
| classify_junc_tx | Man page Source code |
| combine_mut_junc | Man page Source code |
| effect_to_junction_rules | Man page |
| effect_to_junction_rules_wo_ir | Man page |
| exon_in_intron | Man page Source code |
| filter_irfinder_txt | Man page Source code |
| format_cispliceai_thresh | Man page Source code |
| format_pangolin | Man page Source code |
| format_spliceai | Man page Source code |
| format_spliceai_thresh | Man page Source code |
| generate_combined_dataset | Man page Source code |
| generate_junction_id | Man page Source code |
| get_exon_inclusion_junction | Man page Source code |
| get_exon_skipping_junction | Man page Source code |
| get_intronretention_alt_pos | Man page Source code |
| get_intronretention_genomic_alt_pos | Man page Source code |
| get_junc_pos | Man page Source code |
| get_normalized_protein_junc_pos | Man page Source code |
| get_peptide_context | Man page Source code |
| get_unknown_exon_intron_retention | Man page Source code |
| import_irfinder_txt | Man page Source code |
| import_leafcutter_counts | Man page Source code |
| import_regtools_junc | Man page Source code |
| import_spladder | Man page Source code |
| import_star_sj | Man page Source code |
| import_stringtie_gtf | Man page Source code |
| is_canonical | Man page Source code |
| is_first_reading_frame | Man page Source code |
| is_in_rnaseq | Man page Source code |
| is_start_on_exon | Man page Source code |
| junc2breakpoint | Man page Source code |
| junc_to_gr | Man page Source code |
| leafcutter_transform | Man page Source code |
| liftover_junc_id | Man page Source code |
| map_requant | Man page Source code |
| modify_tx | Man page Source code |
| next_junctions | Man page Source code |
| pangolin_effect_translation | Man page |
| parse_cispliceai_thresh | Man page Source code |
| parse_gtf | Man page Source code |
| parse_irfinder_txt | Man page Source code |
| parse_mmsplice | Man page Source code |
| parse_pangolin | Man page Source code |
| parse_spliceai | Man page Source code |
| parse_spliceai_thresh | Man page Source code |
| parse_star_sj | Man page Source code |
| read_requant | Man page Source code |
| read_suppa_ioe | Man page Source code |
| regtools_transform | Man page Source code |
| seq_truncate_nonstop | Man page Source code |
| sort_columns | Man page Source code |
| spladder_transform | Man page Source code |
| spladder_transform_ass | Man page Source code |
| spladder_transform_exon_skipping | Man page Source code |
| spladder_transform_format | Man page Source code |
| spladder_transform_intron_retention | Man page Source code |
| spladder_transform_mutex_exon | Man page Source code |
| stringtie_transform | Man page Source code |
| stringtie_transform_format | Man page Source code |
| suppa_import | Man page Source code |
| suppa_transform | Man page Source code |
| suppa_transform_format | Man page Source code |
| toy_cds | Man page |
| toy_junc_df | Man page |
| toy_junc_id | Man page |
| toy_junc_id_enst | Man page |
| toy_transcripts | Man page |
| toy_transcripts_gr | Man page |
| transform_for_requant | Man page Source code |
| transform_irfinder_txt | Man page Source code |
| transform_leafcutter_counts | Man page Source code |
| transform_regtools_junc | Man page Source code |
| transform_star_sj | Man page Source code |
| transform_suppa_ass_events | Man page Source code |
| transform_suppa_ir_events | Man page Source code |
| transform_suppa_mxe_events | Man page Source code |
| transform_suppa_se_events | Man page Source code |
| unique_junc_mmsplice | Man page Source code |
| unique_mut_junc | Man page Source code |
| unsorted_junc_df | Man page |
