Skip to contents

Version 0.5

AcidGenerics 0.5.0 (2020-12-22)

Major changes:

  • Now reexporting S4 generics defined in BiocGenerics and S4Vectors that are used to define methods inside Acid Genomics R packages.
  • Importing Biobase package, which defines sampleNames and sampleNames<- generics.
  • Migrated some generics previously defined in basejump: integerCounts, makeSampleData.
  • Need to reexport colSums, rowSums, and unlist from BiocGenerics.
  • Now importing AsIs S4 class defined in BiocGenerics.
  • Importing additional S4 generics defined in S4Vectors that are in use internally inside basejump.
  • Migrated generics previously defined in bcbioRNASeq: as.DESeqDataSet, as.DESeqTransform, as.DGEList, plotPseudoVsAlignedCounts, and slotAlignedCounts.
  • Added unlistToDataFrame, which is being added to AcidPlyr.

AcidGenerics 0.5.1 (2021-01-15)

New functions:

  • Added some useful matching generics, which will be deployed in Acid Generics packages to avoid hard-coding identifier column names: matchCellColumn, matchGeneColumn, matchSampleColumn, and matchTranscriptColumn.

Deprecations:

  • Deprecated matchRowNameColumn in favor if matchRownameColumn (note case).

AcidGenerics 0.5.2 (2021-01-21)

New functions:

  • geneIDs (complementing previous geneNames generic), transcriptIDs, transcriptNames, stripGeneVersions, (complementing previous stripTranscriptVersions generic), and a new stripVersions generic that is intended to sanitize both genes and transcripts in a single call.

AcidGenerics 0.5.3 (2021-01-25)

Minor changes:

  • Reexporting is.unsorted and sort from BiocGenerics.

AcidGenerics 0.5.4 (2021-02-02)

Major changes:

  • Made markdown and mcolnames generics defunct.

AcidGenerics 0.5.5 (2021-02-02)

New generics:

  • Created new generics for rankedMatrix and showHeader, which are now defined in AcidBase. Previously, these functions were defined in basejump.

Minor changes:

  • geometricMean: Renamed primary argument from “object” to “x”, better matching the conventions used by mean and sem.

AcidGenerics 0.5.6 (2021-02-05)

New classes:

  • Exporting missingOrNULL class, previously defined internally in basejump.
  • Also now reexporting Annotated class from S4Vectors.

AcidGenerics 0.5.7 (2021-02-08)

New functions:

  • Reexporting unsplit from BiocGenerics.

AcidGenerics 0.5.8 (2021-02-08)

New functions:

  • Include var reexport, which is used in AcidPlots.

AcidGenerics 0.5.9 (2021-02-09)

New functions:

  • Reexporting some additional Bioconductor generics: head, summary, tail.
  • plotCorrelation: New X-Y scatterplot correlation plotting generic.

AcidGenerics 0.5.10 (2021-02-10)

New functions:

  • Reexporting cbind and rbind from Bioconductor.

AcidGenerics 0.5.11 (2021-02-11)

Minor changes:

  • Consolidate all S4Vectors class and function reexports here. Some were previously defined in pipette.

AcidGenerics 0.5.12 (2021-02-12)

Minor changes:

  • Now reexporting end, start, and width from BiocGenerics.
  • Also reexporting grep and grepl from BiocGenerics, which is needed for downstream operations on CharacterList in AcidGenomes.

AcidGenerics 0.5.13 (2021-02-12)

Major changes:

  • Now including IRanges in package.
  • Including more reexports that are defined in S4Vectors and BiocGenerics.

AcidGenerics 0.5.14 (2021-02-13)

Minor changes:

  • Added more Bioconductor generic reexports.
  • Reorganized Bioconductor generics with roxygen documentation.

AcidGenerics 0.5.15 (2021-02-20)

New functions:

  • Now exporting mapToDataFrame and rbindToDataFrame, which have methods (i.e. for list) defined in AcidPlyr update.

Minor changes:

  • Deprecating unlistToDataFrame in favor of mapToDataFrame.

AcidGenerics 0.5.16 (2021-02-22)

New functions:

  • Including getListElement from S4Vectors, which is used in bcbioRNASeq.

AcidGenerics 0.5.17 (2021-02-22)

New functions:

  • Reexporting sapply, which is used in pointillism.

AcidGenerics 0.5.18 (2021-06-20)

New functions:

  • Reexporting median and quantile, which are defined in IRanges. These generics are very useful when operating on NumericList objects.

AcidGenerics 0.5.19 (2021-08-24)

Minor changes:

  • Now requiring Bioconductor 3.13+ to be installed.

AcidGenerics 0.5.20 (2021-09-08)

Minor changes:

  • Removing deprecated functions from the NAMESPACE, to clean up and lighten the package a bit: clusterCellCountsPerSample, flatFiles, markdown, matchRowNameColumn, mcolnames, meltCounts, plotDot, plotGSEATable, plotGenesDetected, plotGenesPerCell,plotUMIsPerCell, plotUMIsVsGenes, and unlistToDataFrame.