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Version 0.7

AcidGenerics 0.7.0 (2023-09-29)

Major changes:

  • New release series where we are enforcing strict camel case for all generics.
  • Also removed usage of "2" in generic names in favor of "to".
  • Renamed Ensembl2Ncbi to EnsemblToNcbi.
  • Renamed Gene2Symbol to GeneToSymbol.
  • Renamed Ncbi2Ensembl to NcbiToEnsembl.
  • Renamed Tx2Gene to TxToGene.
  • Renamed cell2sample to cellToSample.
  • Renamed plotDEGHeatmap to plotDegHeatmap.
  • Renamed plotDEGPCA to plotDegPca. The word boundary is better here.
  • Renamed plotDEGStackedBar to plotDegStackedBar.
  • Renamed plotDEGUpset to plotDegUpset.
  • Renamed plotLFC to plotLfc.
  • Renamed plotNES to plotNes.
  • Renamed plotPCACovariates to plotPcaCovariates.
  • Renamed plotPCElbow to plotPcElbow.
  • Renamed plotQC to plotQc.
  • Renamed plotRRNAMappingRate to plotRrnaMappingRate. The word boundary looks clearer to me here.
  • Renamed plotTSNE to plotTsne.
  • Renamed plotUMAP to plotUmap.
  • Renamed removeNA to removeNa.
  • Renamed sanitizeNA to sanitizeNa.
  • Now exporting plotMa and plotPca strict camel variants. BiocGenerics uses plotMA and plotPCA, for reference.

Minor changes:

  • Reworked documentation to indicate that headtail should return character.

AcidGenerics 0.7.1 (2023-10-03)

Major changes:

  • Fixed some additional generics that should be in strict camel case.
  • Renamed convertSampleIDsToNames to convertSampleIdsToNames.
  • Renamed geneIDs to geneIds.
  • Renamed mapGenesToIDs to mapGenesToIds.
  • Renamed transcriptIDs to transcriptIds.

AcidGenerics 0.7.2 (2023-10-05)

Major changes:

  • Renamed plotGeneSaturation to plotFeatureSaturation.
  • Removed plotCountsPerGene in favor of plotCountsPerFeature.
  • Removed topTables in favor of markdownTables.

AcidGenerics 0.7.3 (2023-10-06)

New functions:

  • cellsPerGeneFusion: Return the number of cells per gene fusion.
  • cellsPerMutation: Return the number of cells per mutation.
  • excludeNonCancerCells: Exclude non-cancer cells.
  • excludeNonHumanCells: Exclude non-human cells.
  • geneFusions: Gene fusions per cell.
  • mutations: (Driver gene) mutations per cell.

AcidGenerics 0.7.4 (2023-11-30)

New functions:

  • unlist2: Unlist a complex S4 object, such as DFrameList to DFrame.

AcidGenerics 0.7.5 (2023-12-12)

New functions:

  • filterNested: Keep rows that match a nested condition. Performs recursive regular expression matching across all columns, including nested list columns.

AcidGenerics 0.7.6 (2023-12-15)

New functions:

  • matchAll: New variant of match that returns all positional matches for arguments defined in x, rather than only the first match.

AcidGenerics 0.7.7 (2024-03-18)

New functions:

  • stripExonVersions: New generic similar to stripGeneVersions and stripTranscriptVersions.

AcidGenerics 0.7.8 (2024-04-05)

New functions:

  • plotCleveland: Cleveland dot plot generic.

AcidGenerics 0.7.9 (2025-03-21)

Minor changes:

  • Relaxed R dependency down to 4.0 for better backwards compatibility on legacy systems, such as Ubuntu 22 LTS.

AcidGenerics 0.7.10 (2025-04-24)

Minor changes:

  • Reformatted package styling with air conventions.

AcidGenerics 0.7.11 (2026-06-19)

License changes:

  • Relicensed from AGPL-3 to Apache 2.0.

Minor changes:

  • Modernized tooling: refreshed .lintr to the current ruleset, migrated to roxygen2 8.0 (Config/roxygen2/version).