Man pages for avidaR
A Computational Biologist’s Toolkit To Get Data From 'avidaDB'
| convert_org_into_seq | Converts a genome instruction sequence into a digital... |
| convert_seq_into_org | Converts a genome instruction sequence into a digital... |
| get_db_summary | Get database summary |
| get_docker_image_from_experiment_id | Get docker image from experiment |
| get_doi_from_experiment_id | Get doi from experiment |
| get_experiment_id_from_organism_id | Get experiment from organism |
| get_genome_id_from_genome_seq | Get genome from genome sequence |
| get_genome_id_from_logic_operation | Get genome from logic operations |
| get_genome_id_from_phenotype_id | Get genome from phenotype |
| get_genome_id_from_transcriptome_id | Get genome from transcriptome |
| get_genome_id_of_wild_type_organisms | Get genomes of wild-type organisms |
| get_genome_seq_from_genome_id | Get genome sequence from genome |
| get_logic_operation_from_phenotype_id | Get the logic operations computed by a digital organism whose... |
| get_mutant_at_pos | Get single-point mutants of wild-type organisms |
| get_phenotype_id_from_genome_id | Get phenotype from genome |
| get_phenotype_id_from_genome_seq | Get phenotype from genome sequence |
| get_phenotype_id_from_logic_operation | Get phenotype from logic operations |
| get_phenotype_id_from_transcriptome_id | Get phenotype from transcriptome |
| get_tandem_id_from_genome_id | Get tandem repeat from genome |
| get_tandem_id_from_genome_seq | Get tandem repeat from genome sequence |
| get_tandem_id_from_logic_operation | Get tandem repeat from logic operations |
| get_tandem_id_from_phenotype_id | Get tandem repeat from phenotype |
| get_tandem_seq_from_tandem_id | Get the tandem repeat sequence from tandem repeat |
| get_transcriptome_id_from_genome_id | Get transcriptome from genome |
| get_transcriptome_id_from_genome_seq | Get transcriptome from genome sequence |
| get_transcriptome_id_from_logic_operation | Get transcriptome from logic operations |
| get_transcriptome_id_from_phenotype_id | Get transcriptome from phenotype |
| get_transcriptome_seq_from_transcriptome_id | Get transcriptome sequence from transcriptome |
| instruction_set | Get the genetic language of Avida |
| logic_operation | Get the list of logic operations that a digital organism can... |
| plot_transcriptome | Get a plot of the transcriptome as a chord diagram |
| triplestore_access | Class to manage triplestore access options |
