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

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Documentation for package ‘avidaR’ version 1.1.3

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convert_seq_into_org Converts a genome instruction sequence into a digital organism file
get_db_summary Get database summary
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