API for arendsee/fagin
Annotate Orphan Genes
| Global functions | |
|---|---|
| .determine_labels | Source code |
| .determine_origins | Source code |
| .dnaregex_unstranded | Source code |
| .extract | Source code |
| .get_gc | Source code |
| .label | Source code |
| .rbindlist | Source code |
| .select_tag | Source code |
| AA_aln | Source code |
| MakeGI | Source code |
| align_by_map | Source code |
| aln_xy | Source code |
| buildFeatureTable | Source code |
| buildLabelsTree | Source code |
| by_primary | Source code |
| by_secondary | Source code |
| check_for_incomplete_models | Source code |
| check_for_internal_stops | Source code |
| check_protein_transcript_match | Source code |
| classify | Source code |
| compare_target_to_focal | Source code |
| config | Man page Source code |
| config_alignment | Man page |
| config_alignment-class | Man page |
| config_alignment_simulation | Man page |
| config_alignment_simulation-class | Man page |
| config_alignment_thresholds | Man page |
| config_alignment_thresholds-class | Man page |
| config_get_tree_file | Source code |
| 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 | Source code |
| convert_GRanges_to_SynderGFF | Source code |
| default_class_rule | 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 |
| determine_labels | Man page Source code |
| determine_origins | Man page Source code |
| dgumbel | Man page Source code |
| dna_summary | Man page |
| dna_summary-class | Man page |
| dnaregex | Man page Source code |
| extract_phase_from_GRangesList | Source code |
| extract_with_complements | Man page |
| faa_summary | Man page |
| faa_summary-class | Man page |
| fagin | Man page |
| fagin-package | Man page |
| fagin_config | Man page |
| fagin_config-class | Man page |
| fagin_io | Man page |
| fagin_printer | Man page |
| fagin_summary | Man page |
| filter_with_warning__unnamed_entries | Source code |
| filter_with_warnings__zero_length_proteins | Source code |
| final_protein_residue_counts | Man page |
| findFocalSpecies | Source code |
| find_indels | Source code |
| find_initial_phase | Source code |
| fit.gumbel | Source code |
| fuzzy_translate | Source code |
| genomic_composition | Man page |
| get_species | Man page Source code |
| get_species_phylogenetic_order | Man page |
| get_summaries | Man page |
| get_synder_count_table | Man page |
| get_synder_nsi | Man page |
| get_targets | Man page Source code |
| get_trans_dna | Source code |
| gff_summary | Man page |
| gff_summary-class | Man page |
| granges_summary | Man page |
| granges_summary-class | Man page |
| initial_protein_residue_counts | Man page |
| labelTreeToTable | Source code |
| load_dna | Man page Source code |
| load_gene_list | Man page Source code |
| load_gene_models | Man page Source code |
| load_species | Source code |
| load_tree | Man page Source code |
| m_get_proteins | Source code |
| makeAllGenePages | Source code |
| makeGenePage | Source code |
| make_excel_spreadsheet | Man page |
| make_fagin_cacher | Man page Source code |
| make_format_translation_warning | Man page Source code |
| make_genome_table | Man page |
| make_numeric_summary_table | Source code |
| make_origin_table | Man page |
| make_query_target_table | Man page |
| make_result_archive | Man page |
| make_secondary_genewise_table | Man page |
| make_secondary_labels_table | Man page |
| make_seqinfo | Source code |
| make_synder_flag_table | Man page |
| make_synder_table | Man page |
| make_synmap_table | Man page |
| merge_named_vectors | Man page Source code |
| nothing | Source code |
| number_of_scaffolds | Man page |
| numeric_summary | Man page |
| numeric_summary-class | Man page |
| overlapMap | Source code |
| pgumbel | Man page Source code |
| phase_summary | Man page |
| phase_summary-class | Man page |
| plotDecisionTree | Source code |
| plot_secondary_labels | Man page |
| prettyCat | Source code |
| prettyCatList | Source code |
| prettyTable | Source code |
| prettyVector | Source code |
| primary_data | Man page |
| print.config_alignment | Man page Source code |
| print.config_alignment_simulation | Man page Source code |
| print.config_alignment_thresholds | Man page Source code |
| print.config_input | Man page Source code |
| print.config_orf | Man page Source code |
| print.config_synder | Man page Source code |
| print.derived_input | Source code |
| print.dna_summary | Source code |
| print.faa_summary | Source code |
| print.fagin_config | Man page Source code |
| print.gff_summary | Source code |
| print.numeric_summary | Man page Source code |
| print.seq_summary | Source code |
| print.species_data_files | Source code |
| print.species_meta | Source code |
| print.species_summaries | Source code |
| print.synmap_summary | Source code |
| protein_has_internal_stop | Man page |
| qgumbel | Man page Source code |
| rownames_as_species | Source code |
| run_fagin | Man page Source code |
| secondary_data | Man page |
| seq_summary | Man page |
| seq_summary-class | Man page |
| setAncestor | Source code |
| 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 |
| tertiary_data | Man page Source code |
| top_class | Source code |
| trim_CDS_with_non_zero_phase | Source code |
| validate_config | Man page Source code |
| yeast_config | Man page Source code |
