Package: avidaR 1.2.1

Raúl Ortega

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

Easy-to-use tools for performing complex queries on 'avidaDB', a semantic database that stores genomic and transcriptomic data of self-replicating computer programs (known as digital organisms) that mutate and evolve within a user-defined computational environment.

Authors:Miguel A. Fortuna [aut], Raúl Ortega [cre]

avidaR_1.2.1.tar.gz
avidaR_1.2.1.tar.gz(r-4.5-noble)avidaR_1.2.1.tar.gz(r-4.4-noble)
avidaR_1.2.1.tgz(r-4.4-emscripten)avidaR_1.2.1.tgz(r-4.3-emscripten)
avidaR.pdf |avidaR.html✨
avidaR/json (API)
NEWS

# Install 'avidaR' in R:
install.packages('avidaR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://gitlab.com/fortunalab/avidar

1.70 score 2 scripts 283 downloads 32 exports 45 dependencies

Last updated 6 months agofrom:fd976f3575. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-linuxOKDec 21 2024

Exports:convert_org_into_seqconvert_seq_into_orgget_db_summaryget_docker_image_from_experiment_idget_doi_from_experiment_idget_experiment_id_from_organism_idget_genome_id_from_genome_seqget_genome_id_from_logic_operationget_genome_id_from_phenotype_idget_genome_id_from_transcriptome_idget_genome_id_of_wild_type_organismsget_genome_seq_from_genome_idget_logic_operation_from_phenotype_idget_mutant_at_posget_phenotype_id_from_genome_idget_phenotype_id_from_genome_seqget_phenotype_id_from_logic_operationget_phenotype_id_from_transcriptome_idget_tandem_id_from_genome_idget_tandem_id_from_genome_seqget_tandem_id_from_logic_operationget_tandem_id_from_phenotype_idget_tandem_seq_from_tandem_idget_transcriptome_id_from_genome_idget_transcriptome_id_from_genome_seqget_transcriptome_id_from_logic_operationget_transcriptome_id_from_phenotype_idget_transcriptome_seq_from_transcriptome_idinstruction_setlogic_operationplot_transcriptometriplestore_access

Dependencies:askpassbase64encbitbit64circlizeclicliprcolorspacecpp11crayoncurldplyrfansigenericsGlobalOptionsgluehmshttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangshapestringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrxml2

Readme and manuals

Help Manual

Help pageTopics
Converts a genome instruction sequence into a digital organism fileconvert_org_into_seq
Converts a genome instruction sequence into a digital organism fileconvert_seq_into_org
Get database summaryget_db_summary
Get docker image from experimentget_docker_image_from_experiment_id
Get doi from experimentget_doi_from_experiment_id
Get experiment from organismget_experiment_id_from_organism_id
Get genome from genome sequenceget_genome_id_from_genome_seq
Get genome from logic operationsget_genome_id_from_logic_operation
Get genome from phenotypeget_genome_id_from_phenotype_id
Get genome from transcriptomeget_genome_id_from_transcriptome_id
Get genomes of wild-type organismsget_genome_id_of_wild_type_organisms
Get genome sequence from genomeget_genome_seq_from_genome_id
Get the logic operations computed by a digital organism whose genome encodes a specific phenotypeget_logic_operation_from_phenotype_id
Get single-point mutants of wild-type organismsget_mutant_at_pos
Get phenotype from genomeget_phenotype_id_from_genome_id
Get phenotype from genome sequenceget_phenotype_id_from_genome_seq
Get phenotype from logic operationsget_phenotype_id_from_logic_operation
Get phenotype from transcriptomeget_phenotype_id_from_transcriptome_id
Get tandem repeat from genomeget_tandem_id_from_genome_id
Get tandem repeat from genome sequenceget_tandem_id_from_genome_seq
Get tandem repeat from logic operationsget_tandem_id_from_logic_operation
Get tandem repeat from phenotypeget_tandem_id_from_phenotype_id
Get the tandem repeat sequence from tandem repeatget_tandem_seq_from_tandem_id
Get transcriptome from genomeget_transcriptome_id_from_genome_id
Get transcriptome from genome sequenceget_transcriptome_id_from_genome_seq
Get transcriptome from logic operationsget_transcriptome_id_from_logic_operation
Get transcriptome from phenotypeget_transcriptome_id_from_phenotype_id
Get transcriptome sequence from transcriptomeget_transcriptome_seq_from_transcriptome_id
Get the genetic language of Avidainstruction_set
Get the list of logic operations that a digital organism can computelogic_operation
Get a plot of the transcriptome as a chord diagramplot_transcriptome
Class to manage triplestore access optionstriplestore_access