freerange 0.1.0 (2019-03-27)

Initial release. Migrated Ensembl AnnotationHub and GFF/GTF parsing functions here from the basejump package.

freerange 0.1.1 (2019-03-28)

Minor changes

  • Renamed organism_mappings data to organismMappings, to improve camel case consistency in package.

freerange 0.1.2 (2019-04-07)

Major changes

  • emptyRanges: Renamed mcolsNames to mcolnames, for better consistency with the basejump naming conventions. Note that this formal is currently used by basejump and bcbioSingleCell.

Minor changes

  • Reworked unit tests to improve code coverage above 90%.
  • Added back data-raw/ scripts used to general minimal GFF example files.
  • .makeGenesFromEnsemblGTF and .makeTranscriptsFromEnsemblGTF: Made assert checks less strict. No longer requiring gene_biotype or gene_name, so we can pass through GRanges generated from FlyBase or WormBase.

Future considerations

  • Still not removing gene and transcript version numbers for GENCODE GFF files. Consider changing this convention in a future update.

freerange 0.1.3 (2019-04-22)

Minor changes

  • Backward compatibility fixes/updates for BioC 3.6 / R 3.4.

freerange 0.1.4 (2019-04-25)

Minor changes

  • S4 generic reexport documentation fixes.

freerange 0.1.5 (2019-05-02)

Minor changes

  • makeGRangesFromEnsembl: Detect organisms with complex names including 3 words (e.g. Canis lupus familiaris) and automatically sanitize to the 2 word convention used internally by ensembldb (e.g. Canis familiaris). Thanks @umasaxena for the heads up on this.

freerange 0.1.6 (2019-05-06)

Major changes

  • Now pinned to R >= 3.5.

Minor changes

  • Updated basejump dependencies, reflecting change in brio package.