avidaR 1.2.1

Bug fixes

• Fix Language field value: invalid ‘en_US’ value replaced by ‘en-US’.
• Fix CRAN URL for avidaR package not in canonical form.
• Fix possibly non valid URL.

avidaR 1.2.0

New features

• Added function convert_org_into_seq to convert a digital organism file into a genome instruction sequence.
• Added function get_doi_from_experiment_id to get the DOI of the scientific publication that documents the experiment carried out.
• Added function get_experiment_id_from_organism_id to get the experiment identifier from which a digital organism is derived.
• Added function get_docker_image_from_experiment_id to get the docker image built to run the experiment, which guarantees reproducibility.

Improvements

• Updated colors for better comprehension on figures generated by plot_transcriptome() function.
• The plot_transcriptome function can now plot multiple transcriptomes in a single function call.
• The instruction_set function has been extended to use the “head”, “head-sex”, and “transsmt” instruction sets.

Bug fixes

• Fixed issues to comply with the CRAN policy: ‘Packages which use Internet resources should fail gracefully with an informative message if the resource is not available or has changed (and not give a check warning nor error)’.
• Fixed issue ‘Use of .data in tidyselect expressions was deprecated’ on convert_seq_into_org() function.

avidaR 1.1.3

Improvements

• More friendly error messages for helping in solving issues caused by service availability, not valid user requests, unauthorized access, and others.

New features

• Added timeout parameter in method set_access_options() to limit the amount of time waiting data from the service.

Bug fixes

• Removed top-level code which creates triplestore object and set default access options. Read more about how to properly connect to ‘avidaDB’.

avidaR 1.1.2

Improvements

• If seed_id is not specified, a randomly-chosen seed_id value is used to speed up the execution of the following functions:
  • get_genome_id_from_logic_operation
  • get_genome_id_from_phenotype_id
  • get_transcriptome_id_from_logic_operation
  • get_transcriptome_id_from_phenotype_id
  • get_transcriptome_id_from_logic_operation
  • get_transcriptome_id_from_phenotype_id
• The function get_mutant_at_pos has been expanded:
  • The function parameter genome_id has been added, and the previous parameters (inst_replaced , inst_replaced_by, and pos) can be now omitted by the user.
  • If genome_id is not specified, a randomly chosen genome_id (between those provided by the function get_genome_id_of_wild_type_organisms) will be used.
  • If inst_replaced and/or inst_replaced_by is/are not specified, all mutations at the specified position on the genome are shown.
  • If the parameter pos is not specified, all mutations at all positions on the genome are shown (depending on the values of inst_replaced and inst_replaced_by).

New features

• Added function get_db_summary that will provide a summary of the database.
• Added get_genome_id_of_wild_type_organisms to identify the genomes of the organisms that were used as wild-type organisms.

Bug fixes

• Removed a line from the clause WHERE that was slowing down the execution of the function get_transcriptome_id_from_phenotype_id.
• The use of exponential notation was prevented because it provided empty results when requesting data by identifiers like genome_10000000.

avidaR 1.0.1

• Initial release #’