API for HajkD/orthologr
Comparative Genomics with R
| Global functions | |
|---|---|
| Different | Source code |
| NotAGap | Source code |
| NumDiffs | Source code |
| OF2Orthologs | Source code |
| TranslateCodon | Source code |
| TsTv | Source code |
| Universal | Source code |
| ambigousNucleotides | Source code |
| blast | Man page Source code |
| blast_best | Man page Source code |
| blast_rec | Man page Source code |
| cds2aa | Man page Source code |
| check_annotation | Man page Source code |
| check_ram | Source code |
| clean_all_folders | Man page Source code |
| codonPrecondition | Source code |
| codon_aln | Man page Source code |
| compute_dnds | Man page Source code |
| dNdS | Man page Source code |
| diamond | Man page Source code |
| diamond_best | Man page Source code |
| diamond_rec | Man page Source code |
| divergence_map | Man page Source code |
| divergence_stratigraphy | Man page Source code |
| extract_features | Man page Source code |
| filter_best_hits | Man page Source code |
| filter_core_set | Man page Source code |
| filter_core_set_lnc | Man page Source code |
| filter_dNdS | Man page Source code |
| generate_ortholog_tables | Man page Source code |
| generate_ortholog_tables_all | Man page Source code |
| gestimator | Source code |
| get_filename | Source code |
| import_ortholog_tables_all | Man page Source code |
| intToNuc | Source code |
| is.alignment_search_tool | Source code |
| is.codon_aln_tool | Source code |
| is.dnaSequence | Source code |
| is.dnds_est_method | Source code |
| is.multiple_aln_tool | Source code |
| is.ortho_detection_method | Source code |
| is.pairwise_aln_tool | Source code |
| is_installed_blast | Source code |
| is_installed_clustalo | Source code |
| is_installed_clustalw | Source code |
| is_installed_diamond | Source code |
| is_installed_kaks_calculator | Source code |
| is_installed_mafft | Source code |
| is_installed_muscle | Source code |
| is_installed_orthofinder | Source code |
| is_installed_tcoffee | Source code |
| lnc_map_core_orthologs | Man page Source code |
| lnc_map_counts | Man page Source code |
| map_generator_dnds | Man page Source code |
| map_generator_lnc | Man page Source code |
| multi_aln | Man page Source code |
| nucToInt | Source code |
| orthofinder2 | Man page Source code |
| orthofinder2_retrieve_core_orthologs | Man page Source code |
| orthologs | Man page Source code |
| orthologs_lnc | Man page Source code Source code |
| pairwise_aln | Man page Source code |
| plot_diverse_homology_thresholds | Man page Source code |
| plot_diverse_homology_thresholds_core_orthologs | Man page Source code |
| plot_pairwise_orthologs | Man page Source code |
| promotor_divergence_estimation | Man page Source code |
| promotor_divergence_of_orthologous_genes | Man page Source code |
| read.cds | Man page Source code |
| read.dnds.tbl | Man page Source code |
| read.genome | Man page Source code |
| read.ortholog.table | Source code |
| read.proteome | Man page Source code |
| retrieve_core_orthologs | Man page Source code |
| retrieve_longest_isoforms | Man page Source code |
| retrieve_longest_isoforms_all | Man page Source code |
| select_orthologs | Man page Source code |
| set_blast | Man page Source code |
| set_diamond | Man page Source code |
| set_path | Source code |
| substitutionrate | Man page Source code |
| test | Source code |
| testCoreOrthoParamsGeneLocus | Man page Source code |
| testCoreOrthoParamsSpliceVariant | Man page Source code |
| toChar | Source code |
| transl | Man page Source code |
| translate_cds_to_protein | Man page Source code |
| translate_cds_to_protein_all | Man page Source code |
| write.proteome | Man page Source code |
| ws_wrap | Source code |
