R: A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

# A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

## Documentation for package ‘avidaR’ version 1.2.1

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

convert_org_into_seq | Converts a genome instruction sequence into a digital organism file
convert_seq_into_org | Converts a genome instruction sequence into a digital organism file
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 genome encodes a specific phenotype
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 compute
plot_transcriptome | Get a plot of the transcriptome as a chord diagram
triplestore_access | Class to manage triplestore access options