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Version 0.8

AcidGenomes 0.8.0 (2026-05-31)

New functions:

  • goTermsPerGeneName: Import gene ontology (GO) terms per gene name from GOA annotation files.
  • importEnsemblToNcbiGeneMap: Import Ensembl-to-NCBI gene identifier mappings.
  • mapGoTerms: Map GO term identifiers to human-readable names.
  • mapRnacentral: Map gene identifiers to RNAcentral.
  • stripExonVersions: Strip version suffixes from exon identifiers.
  • updateGeneSymbols: Update outdated gene symbols to current nomenclature.

New classes:

  • Added exon-level annotation classes: EnsemblExons, FlybaseExons, GencodeExons, RefseqExons, UcscExons, WormbaseExons.

Major changes:

  • Removed makeGeneToSymbol (all variants: makeGeneToSymbolFromEnsembl, makeGeneToSymbolFromEnsDb, makeGeneToSymbolFromGff) and makeTxToGene (variants: makeTxToGeneFromEnsDb, makeTxToGeneFromEnsembl, makeTxToGeneFromGff). Use makeGRangesFromEnsembl() or makeGRangesFromEnsDb() composed with GeneToSymbol() or TxToGene() directly. makeTxToGeneFromFasta() remains.
  • Reworked internal gene mapping to use NcbiGeneInfo dbXrefs, improving reliability of Ensembl-to-NCBI identifier mapping.
  • Enabled case-insensitive gene name matching in mapping functions.

Minor changes:

  • Code reformatted with the air R formatter.

License changes:

  • Switched from AGPL-3.0 to Apache-2.0.

AcidGenomes 0.8.1 (2026-06-19)

Minor changes:

  • Modernized tooling: removed per-package .lintr in favour of global ~/.lintr; added air.toml; migrated to roxygen2 8.0.

AcidGenomes 0.8.2 (2026-09-18)

Bug fixes:

  • Restore Ensembl reference-genome downloads by using the supported HTTPS transport instead of FTP.
  • Restore automatic Ensembl release detection using the machine-readable VERSION endpoint.
  • Replace the unavailable useast.ensembl.org archive endpoint with the canonical Ensembl website endpoint.