API for lijing28101/fagin2
Annotate Orphan Genes
| Global functions | |
|---|---|
| .dnaregex_unstranded | Man page Source code |
| .label | Man page Source code |
| AA_aln | Man page Source code |
| MakeGI | Man page Source code |
| add_gene | Man page Source code |
| alignToGenome | Man page |
| align_by_map | Man page Source code |
| aln_xy | Man page Source code |
| buildFeatureTable | Man page Source code |
| buildLabelsTree | Man page Source code |
| calculate_match_significance | Man page |
| check_for_incomplete_models | Man page Source code |
| check_for_internal_stops | Man page Source code |
| check_protein_transcript_match | Man page Source code |
| compare_target_to_focal | Man page Source code |
| config | Man page Source code |
| config_alignment | Man page |
| config_alignment-class | Man page |
| config_alignment_alnrate | Man page |
| config_alignment_alnrate-class | Man page |
| config_alignment_pvalue | Man page |
| config_alignment_pvalue-class | Man page |
| config_alignment_simulation | Man page |
| config_alignment_simulation-class | Man page |
| config_input | Man page |
| config_input-class | Man page |
| config_orf | Man page |
| config_orf-class | Man page |
| config_synder | Man page |
| config_synder-class | Man page |
| convert_FaFile_to_XStringSet | Man page Source code |
| convert_GRanges_to_SynderGFF | Man page Source code |
| derive_genomic_ORFs | Man page |
| derive_nstring | Man page |
| derive_transcript_ORFs | Man page |
| derived_input | Man page |
| derived_input-class | Man page |
| dgumbel | Man page Source code |
| dna_summary | Man page |
| dna_summary-class | Man page |
| dnaregex | Man page Source code |
| extract_phase_from_GRangesList | Man page Source code |
| extract_range | Man page |
| extract_with_complements | Man page |
| faa_summary | Man page |
| faa_summary-class | Man page |
| fagin_config | Man page |
| fagin_config-class | Man page |
| fagin_io | Man page |
| fagin_summary | Man page |
| filter_with_warning__unnamed_entries | Man page Source code |
| filter_with_warnings__zero_length_proteins | Man page Source code |
| find_indels | Man page Source code |
| fit.gumbel | Man page Source code |
| fix_names | Man page |
| fuzzy_translate | Man page Source code |
| gene_check | Man page Source code |
| getORFs | Man page |
| get_alignment_table | Man page Source code |
| get_dna2dna | Man page |
| get_gff_from_txdb | Man page Source code |
| get_hits_info | Man page Source code |
| get_logmn | Man page |
| get_query_position | Man page Source code |
| get_species | Man page Source code |
| get_target_mRNA_position | Man page Source code |
| get_target_position | Man page Source code |
| get_trans_dna | Man page Source code |
| gff_summary | Man page |
| gff_summary-class | Man page |
| granges_summary | Man page |
| granges_summary-class | Man page |
| labelTreeToTable | Man page Source code |
| load_dna | Man page Source code |
| load_gene_list | Man page Source code |
| load_gene_models | Man page Source code |
| load_species | Man page Source code |
| load_tree | Man page Source code |
| make_seqinfo | Man page Source code |
| merge_feature_table | Man page Source code |
| numeric_summary | Man page |
| numeric_summary-class | Man page |
| overlapMap | Man page Source code |
| pgumbel | Man page Source code |
| phase_summary | Man page |
| phase_summary-class | Man page |
| qgumbel | Man page Source code |
| run_fagin | Man page Source code |
| run_fagin_add | Man page Source code |
| run_fagin_parallel | Man page Source code |
| secondary_data | Man page |
| secondary_data_add | Man page Source code |
| seq_summary | Man page |
| seq_summary-class | Man page |
| species_data_files | Man page |
| species_data_files-class | Man page |
| species_meta | Man page |
| species_meta-class | Man page |
| species_summaries | Man page |
| species_summaries-class | Man page |
| summarize_dna | Man page Source code |
| summarize_faa | Man page Source code |
| summarize_gff | Man page Source code |
| summarize_granges | Man page Source code |
| summarize_nstring | Man page Source code |
| summarize_numeric | Man page Source code |
| summarize_phase | Man page Source code |
| summarize_syn | Man page Source code |
| synmap_summary | Man page |
| synmap_summary-class | Man page |
| synteny_meta | Man page |
| synteny_meta-class | Man page |
| trim_CDS_with_non_zero_phase | Man page Source code |
| validate_config | Man page Source code |
