Man pages for HajkD/orthologr
Comparative Genomics with R
| blast | Perform a BLAST+ search |
| blast_best | Perform a BLAST+ best hit search |
| blast_rec | Perform a BLAST+ reciprocal best hit (RBH) search |
| cds2aa | Translate CDS file to Amino Acids file |
| check_annotation | Check whether an annotation file contains outlier lines |
| clean_all_folders | Delete the internal folder hierarchy |
| codon_aln | Compute a Codon Alignment |
| compute_dnds | Compute dNdS Values For A Given Pairwise Alignment |
| diamond | Perform a DIAMOND2 search |
| diamond_best | Perform a DIAMOND2 best hit search |
| diamond_rec | Perform a DIAMOND2 reciprocal best hit (RBH) search |
| divergence_map | Sort dNdS Values Into Divergence Strata |
| divergence_stratigraphy | Perform Divergence Stratigraphy |
| dNdS | Compute dNdS values for two organisms |
| extract_features | Helper function to extract gene loci and splice variant IDs... |
| filter_best_hits | Helper function to select best BLAST hit based on minimum... |
| filter_core_set | Helper function to extract a core set of orthologous gene... |
| filter_core_set_lnc | Helper function to extract a core set of orthologous lncRNAs |
| filter_dNdS | Filter dNdS values |
| generate_ortholog_tables | Generate ortholog tables by gene locus and splice varaint |
| generate_ortholog_tables_all | Generate ortholog tables by gene locus and splice varaint for... |
| import_ortholog_tables_all | Importing output pairwise orthologs tables generated with... |
| lnc_map_core_orthologs | Retrieve a core set of orthologous lncRNAs from the pairwise... |
| lnc_map_counts | Count number of orthologous lncRNAs per pairwise species... |
| map_generator_dnds | Generate dNdS Maps Between a Query Organism and Multiple... |
| map_generator_lnc | Infer orthologous lncRNAs between multiple species |
| multi_aln | Compute Multiple Sequence Alignments |
| orthofinder2 | Interface function to Orthofinder2 |
| orthofinder2_retrieve_core_orthologs | Retrieve core orthologs across multiple species from... |
| orthologs | Main Orthology Inference Function |
| orthologs_lnc | Orthology Inference of lncRNAs |
| pairwise_aln | Compute Pairwise Alignments |
| plot_diverse_homology_thresholds | Diverse line plots visualizing the number of pairwise... |
| plot_diverse_homology_thresholds_core_orthologs | Diverse line plots visualizing the number of core orthologs... |
| plot_pairwise_orthologs | A line plot visualizing the number of pairwise orthologs... |
| promotor_divergence_estimation | Estimate the DNA distance between promotor sequences |
| promotor_divergence_of_orthologous_genes | Compute promotor sequence divergence of orthologous genes |
| read.cds | Read the CDS of a given organism |
| read.dnds.tbl | Import a dNdS table generated with 'dNdS' |
| read.genome | Read the genome of a given organism |
| read.proteome | Read the proteome of a given organism |
| retrieve_core_orthologs | Retrieve a core set of orthologous gene loci from several... |
| retrieve_longest_isoforms | Retrieve the longest isoforms from a proteome file and save... |
| retrieve_longest_isoforms_all | Retrieve the longest isoforms of several proteome files... |
| select_orthologs | Select orthologs based on either gene locus or splice variant |
| set_blast | Create a BLASTable database with makeblastdb |
| set_diamond | Create a DIAMONDable database with 'diamond makedb' |
| substitutionrate | Internal function for dNdS computations |
| testCoreOrthoParamsGeneLocus | Helper function for... |
| testCoreOrthoParamsSpliceVariant | Helper function for splice variant based... |
| transl | Translate DNA to Amino Acids |
| translate_cds_to_protein | Translate coding sequences into amino acid sequences |
| translate_cds_to_protein_all | Translate coding sequences into amino acid sequences for... |
| write.proteome | Save a proteome in fasta format |
