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Version 0.6

AcidGenomes 0.6.0 (2023-10-04)

New functions / classes:

  • HumanToMouse: Downloads human-to-mouse gene mappings from the Jackson Laboratory MGI server. Returns with unique 1:1 mappings by default, which can be disabled with the unique argument.

Major changes:

  • Renamed some identifier classes to use "To" instead of the numeric "2" in the class name. Sorry Prince, but this just looks weird for some functions. Applies to Ensembl2Ncbi, Gene2Symbol, Ncbi2Ensembl, Protein2Gene, and Tx2Gene.
  • Hardened class checks via validObject for our custom classes, ensuring that metadata is consistently slotted, including date and package version.
  • Switched to HTTPS downloads internally for some functions, as the Ensembl FTP server has been prone to timeouts lately. This does not affect our primary genome downloading functions, which still use FTP for speed.

Minor changes:

  • Migrated internal data from inst/extdata to save internally inside the package via sysdata.rda file. Applies to detectOrganism and mapNcbiTaxId currently.

AcidGenomes 0.6.1 (2023-10-13)

Minor changes:

  • Renamed HumanToMouse to JaxHumanMouse, which indicates the source (Jackson Laboratory) more clearly.
  • Bug fixes for GENCODE and RefSeq genome downloads.