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.