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Version 0.7

AcidGenomes 0.7.0 (2023-12-04)

Major changes:

  • EnsemblToNcbi and NcbiToEnsembl: Added support for disabling strict mode, which is useful for mapping all genes in a reference genome. This is not a breaking change, as strict mode remains enabled by default. Also reworked the internal code to speed up 1:1 mapping return.

Minor changes:

  • Hgnc: Renamed "symbol" column to "geneName" and "name" to "description", better matching naming conventions in other functions.

AcidGenomes 0.7.1 (2023-12-05)

Minor changes:

  • makeGRangesFromEnsembl: Fixed support for legacy GRCh38 release 87 dataset, which doesn’t have gene versions defined, and would otherwise error if ignoreVersion = FALSE is set.

AcidGenomes 0.7.2 (2023-12-06)

Minor changes:

  • makeGRangesFromGff: Don’t error on Seqinfo download failure from Ensembl via getChromInfoFromEnsembl. This is fragile for old GFF files currently, such as "Mus_musculus.GRCm38.90.gtf.gz". We have filed a bug report with Bioconductor for GenomeInfoDb, but we may need to write our own variant of this function that provides better support for old Ensembl releases. Consider referring to ensembldb code for an alternate approach.

AcidGenomes 0.7.3 (2025-03-25)

Minor changes:

  • Relaxed R dependency from 4.3 to 4.0 for backwards compatibility.

AcidGenomes 0.7.4 (2025-04-03)

Minor changes:

  • makeGRangesFromEnsembl: Fix for extraMcols = TRUE mode failure for Homo sapiens when a release, such as Ensembl 112 contains MySQL core files for both GRCh38 ("homo_sapiens_core_112_38") and GRCh37 ("homo_sapiens_core_112_37").

AcidGenomes 0.7.5 (2025-04-07)

Minor changes:

  • mapGeneNamesToEnsembl, mapGeneNamesToHgnc, mapGeneNamesToNcbi: Improved error messages on mapping failure.
  • mapGeneNamesToHgnc: Improved handling for Homo sapiens when genomeBuild and release arguments are defined.