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Version 0.3

acidgenerics 0.3.0 (2020-01-18)

Major changes:

  • Renamed package from bioverbs to acidgenerics, in preparation for CRAN submission of multiple Acid Genomics R packages.
  • Migrated S4 generics previously defined in now archived transformer package: as.DataFrame, as.SummarizedExperiment, coerceToList, matchRowNameColumn, and metadata2.

acidgenerics 0.3.1 (2020-01-27)

New functions:

  • Migrated S4 generics previously defined in syntactic package: camelCase, capitalize, dottedCase, kebabCase, makeDimnames, makeLabel, makeNames, makeTitle, makeWords, sentenceCase, snakeCase, and upperCamelCase.

acidgenerics 0.3.2 (2020-01-28)

Minor changes:

  • Documentation fixes to pass CRAN release checks.

acidgenerics 0.3.3 (2020-01-28)

Minor changes:

  • Switched license from MIT to GPL-3.

acidgenerics 0.3.4 (2020-01-30)

Minor changes:

  • aggregateCols, aggregateRows: Renamed primary argument from “object” to “x”, better matching the conventions used in aggregate generic.
  • aggregateCellsToSamples, aggregateReplicates: Also switched from “object” to “x” here, matching aggregate convention.
  • Removed unused aggregateReplicates generic.

acidgenerics 0.3.5 (2020-05-21)

Minor changes:

  • Removed unused rankedList generic. Note that acidgenerics package uses RankedList generic instead.
  • Removed unused pseudobulk generic. Using aggregateCellsToSamples in basejump package instead.

acidgenerics 0.3.6 (2020-06-10)

New functions:

  • Added plotStackedBarPlot generic.

acidgenerics 0.3.7 (2020-06-25)

New functions:

  • Added plotWaterfall generic.

acidgenerics 0.3.7 (2020-07-24)

Minor changes:

  • Maintenance release, increasing R dependency to 4.0.

acidgenerics 0.3.8 (2020-08-04)

New functions:

  • New generics migrated from DESeqAnalysis: baseMeanThreshold, lfcShrink, lfcShrinkType, plotBaseMean, plotDEGStackedBar, resultsDiff, and transformType.

acidgenerics 0.3.10 (2020-08-18)

New functions:

  • degIntersection: Return DEGs ranked by number of intersections.
  • intersectAll: Look for all intersections in a list.
  • intersectionMatrix: Generate an intersection matrix from a list.
  • degPerContrast: Migrated from DESeqAnalysis.

acidgenerics 0.3.11 (2020-09-14)

New functions:

  • splitByLevel: New generic for easy splitting by factor in a data frame.

acidgenerics 0.3.12 (2020-09-21)

New functions:

  • Migrated generics from acidgsea: convertToHuman, geneSet, geneSetResults, leadingEdge, nesThreshold, plotGeneSet.

acidgenerics 0.3.13 (2020-10-01)

New functions:

  • Migrated additional generics from acidgsea: geneSetNames, plotLFC, and plotNES.
  • Added new mapping generics: mapColnames, mapRownames.
  • Added additional mapping generics in use by new cellosaurus and DepMapAnalysis packages: mapCells and mapGenes.

acidgenerics 0.3.14 (2020-10-01)

New functions:

  • Created a new generic for standardizeCells, which is in use in cellosaurus and DepMapAnalysis packages.