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Version 0.3

AcidGenomes 0.3.0 (2022-03-11)

New functions:

  • mapGencodeToEnsembl: Convenience function for mapping human GENCODE release (e.g. 39) to corresponding Ensembl release (e.g. 105).

Minor changes:

  • Reworked NAMESPACE to inherit from Bioconductor packages, migrating from previous approach that used generics defined only in AcidGenerics.
  • Relaxed GenomicRanges mcols column name validity checks to no longer require strict camelCase formatting. This check can run into issues when slotting into a DESeqDataSet object, which appends non-camelCase-formatted columns into the mcols (corresponding to the rowRanges of the object).
  • Migrated some generics to AcidGenerics, and reexporting here (non-breaking change): Ensembl2Entrez, Entrez2Ensembl, Gene2Symbol, Tx2Gene.
  • Updated references from GRanges to GenomicRanges (virtual class) where applicable in the package.
  • Split out documentation on Ensembl2Entrez and Entrez2Ensembl methods into separate files.
  • Increased the verbosity of setMethod calls, particular in the signature argument, where applicable.
  • Calls to AnnotationHub internally now should never prompt the user about whether to create cache directory. This is achieved by setting ask = FALSE internally.
  • Updated internal class checks inside of assert calls to check for GenomicRanges virtual class rather than GRanges.
  • Improved alphabetical sorting of exported S4 methods.
  • Reexporting some additional functions from GenomeInfoDb: Seqinfo, genome, seqinfo, and seqlevels. Note that corresponding assignment methods (if applicable) are intentionally not reexported here.
  • Genome download functions no longer cache using BiocFileCache by default.