bioverbs 0.1.0 (2018-12-22)

Initial release. Migrated S4 generics from basejump and other bioinformatics-oriented packages here to define a simple, stable package similar to BiocGenerics.

bioverbs 0.1.1 (2019-01-04)

Minor changes

bioverbs 0.1.2 (2019-01-05)

Minor changes

  • Documentation improvements.

bioverbs 0.1.3 (2019-01-12)

New generics

  • atomize.
  • factorize.

bioverbs 0.1.4 (2019-01-12)

Minor changes

bioverbs 0.1.5 (2019-02-01)

New generics

  • rankedList.

bioverbs 0.1.6 (2019-02-11)

New generics

  • plotCounts.

Deprecations

  • plotGene is now deprecated in favor of plotCounts.

bioverbs 0.1.7 (2019-02-17)

New generics

  • pseudobulk.

Minor changes

  • plotGenderMarkers: Improved documentation to no longer point to plotGene.

bioverbs 0.1.8 (2019-02-25)

New generics

  • fpkm.
  • kebab.
  • plotIntergenicMappingRate.

bioverbs 0.1.9 (2019-03-22)

Minor changes

bioverbs 0.1.10 (2019-03-23)

Minor changes

  • Removed extra formatting in documentation titles.

bioverbs 0.1.11 (2019-04-06)

New functions

  • mcolnames: Quickly access the column names of mcols slot.

bioverbs 0.1.12 (2019-04-19)

New functions

  • plotCellCountsPerCluster. Used by pointillism.

Deprecations

  • Deprecated plotCountsPerGene in favor of plotCountsPerFeature. This allows for use in packages at transcript or enhancer (locus) level.

bioverbs 0.1.13 (2019-04-19)

Deprecations

  • Made plotGene defunct in favor of plotCounts.
  • Made plotCountsPerGene defunct in favor of plotCountsPerFeature, and plotGenesDetected defunct in favor of plotFeaturesDetected.

bioverbs 0.1.14 (2019-04-23)

New functions

  • resultsMatrix. Currently in use in the DESeqAnalysis package.

bioverbs 0.1.15 (2019-04-26)

New functions

  • plotDEGHeatmap: Currently in use in the DESeqAnalysis package.

bioverbs 0.1.16 (2019-04-30)

New functions

  • alphaThreshold, lfcThreshold: Convenience generics for use in pfgsea package. These generics may also be useful for DESeqAnalysis package in a future update.
  • collectionNames, contrastNames: Generics previously defined in the pfgsea package. These may be generally useful in other contexts.
  • enrichedGeneSets, plotEnrichedUpset, plotEnrichedGeneSets, plotGSEATable: Useful S4 generics previously defined in pfgsea package.

bioverbs 0.1.17 (2019-05-05)

Major changes

  • Now pinned against R >= 3.5.

Minor changes

  • Miscellaneous documentation improvements, to pass BiocCheck.
  • Improved Travis and AppVeyor CI configuration.

bioverbs 0.1.18 (2019-05-06)

Major changes

  • export generic now uses object instead of x, following the style defined in rtracklayer, rather than rio. This change will primarily affect the brio package, but also currently has method support in DESeqAnalysis and pfgsea.