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Version 0.6

AcidGenerics 0.6.0 (2022-03-10)

Major changes:

  • Package now requires R 4.1 and Bioconductor 3.14 release.
  • Reworked export and import generics to inherit from new BiocIO package.
  • Migrated generics from AcidGenomes: Ensembl2Entrez, Entrez2Ensembl, Gene2Symbol, and Tx2Gene.
  • Migrated new generics defined in DESeqAnalysis package: plotContrastScatter and plotLFC.
  • Migrated KnownMarkers generic from AcidSingleCell here.

Minor changes:

  • Reworked documentation for as.DataFrame generic.
  • Include GRanges and GRangesList generators from GenomicRanges package.
  • Also reexporting new BiocFile class from BiocIO package.
  • Now including additional reexports from GenomeInfoDb package: Seqinfo, genome, seqinfo, seqlevels, and seqnames. This are used primarily in the AcidGenomes and AcidGSEA packages.

AcidGenerics 0.6.1 (2022-04-29)

Major changes:

  • Now pinning against R 4.2 as minimum dependency, for Bioconductor 3.15 release.

AcidGenerics 0.6.2 (2022-05-11)

New functions:

  • Added as.Seurat and as.SingleCellExperiment S4 generics, which are now in use in our pointillism package. Don’t reexport these in basejump, as these are also defined as S3 generics in Seurat package.

AcidGenerics 0.6.3 (2022-05-25)

New functions:

  • Reworking markdownPlots and markdownTables as S4 generics. Previously these used a basic list argument in AcidMarkdown package, but these generics are useful in other bioinformatics packages.
  • Soft deprecating topTables in favor of markdownTables usage.

AcidGenerics 0.6.4 (2022-09-16)

New functions:

  • cast: the opposite of melt. Using the naming conventions defined in now deprecated reshape2 package.

AcidGenerics 0.6.5 (2022-11-17)

New functions:

  • euclidean and zscore. For use in pending AcidBase package update.

AcidGenerics 0.6.6 (2023-02-09)

Minor changes:

  • Removed now unused mapToDataFrame, in favor of only rbindToDataFrame.

AcidGenerics 0.6.7 (2023-04-12)

New functions:

  • Ensembl2Ncbi, Ncbi2Ensembl, and matchNested.

Minor changes:

  • Deprecated Ensembl2Entrez and Entrez2Ensembl in favor of Ensembl2Ncbi and Ncbi2Ensembl respectively. This generics will be updated in a forthcoming package update to AcidGenerics.

AcidGenerics 0.6.8 (2023-08-23)

New functions:

AcidGenerics 0.6.9 (2023-09-08)

New functions:

  • keepOnlyAtomicCols: New generic with methods that will be defined in AcidBase for DFrame and data.frame classes.

AcidGenerics 0.6.10 (2023-09-11)

Minor changes:

  • euclidean: Removed requirement of y in the generic.

AcidGenerics 0.6.11 (2023-09-12)

Major changes:

  • Migrated functions from DepMapAnalysis package: excludeContaminatedCells, excludeProblematicCells, plotGeneEffect, plotGeneEffectVsExpression, plotTopGeneEffectPerCell, plotTopGeneEffectPerGroup, predictSensitivity, selectCells, tnbc.

AcidGenerics 0.6.12 (2023-09-20)

New functions:

  • Added unfactorize, the opposite of our factorize generic.
  • Added simpler variants of BiocIO import and export.