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Version 0.14

basejump 0.14.0 (2021-02-06)

Reworked package to simply inherit and reexport functions from other Acid Genomics packages, rather than defining any code directly here.

Major changes:

  • camelCase and upperCamelCase now default to strict = TRUE, reflecting change implemented in syntactic v0.4.4 release.

Minor changes:

  • Consolidated S4 generic imports into AcidGenerics, removing import dependency on BiocGenerics.
  • Removed reexport of mapUCSCBuildToEnsembl, defined in AcidGenomes.

basejump 0.14.1 (2021-02-08)

Minor changes:

  • Now re-exporting some other useful functions from SummarizedExperiment and SingleCellExperiment, which are defined in AcidExperiment and AcidSingleCell respectively.

basejump 0.14.2 (2021-02-09)

New functions:

  • Added more reexports from base/recommended R packages, including grDevices, grid, methods, stats, and utils.

basejump 0.14.3 (2021-02-10)

New functions:

  • Reexporting some functions used downstream in DESeqAnalysis: capture.output, cbind, getS3method, model.matrix, rbind, and relevel.

basejump 0.14.4 (2021-02-11)

Minor changes:

  • Now reexporting additional classes defined in IRanges via pipette: CharacterList, FactorList, IntegerList, LogicalList, NumericList, and RleList.

basejump 0.14.5 (2021-02-11)

Minor changes:

  • Reworked the NAMESPACE to reduce the number of imported packages.

basejump 0.14.6 (2021-02-12)

Minor changes:

  • Now reexporting end, start, and width from AcidGenerics.

basejump 0.14.7 (2021-02-12)

Minor changes:

  • Migrated reexports of IRanges from pipette to AcidGenerics.

basejump 0.14.8 (2021-02-13)

Minor changes:

  • Added more Bioconductor reexports from BiocGenerics and S4Vectors.
  • Updated dependency versions.

basejump 0.14.9 (2021-02-17)

Minor changes:

  • Reexporting formula and untar, which are used in WormBase package.
  • Ensure grDevices, stats, and utils reexports inherit from AcidBase.
  • Updated dependency version cutoffs.

basejump 0.14.10 (2021-02-21)

Minor changes:

  • Now reexporting mapToDataFrame and rbindToDataFrame from AcidPlyr. Note that unlistToDataFrame is now deprecated, in favor of mapToDataFrame, and will be removed in a future release.

basejump 0.14.11 (2021-02-21)

Minor changes:

  • Including URLencode from utils via AcidBase as a reexport, which is used in the Cellosaurus package.

basejump 0.14.12 (2021-02-22)

Minor changes:

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

basejump 0.14.13 (2021-02-22)

Minor changes:

  • Including seqnames in reexports, which is used in bcbioRNASeq.

basejump 0.14.14 (2021-02-24)

Minor changes:

  • Updated dependency versions.
  • Including some additional reexports from AcidGenomes, such as EntrezGeneInfo.

basejump 0.14.15 (2021-02-26)

Minor changes:

  • Deprecated metadataBlacklist in favor of metadataDenylist.
  • Updated dependency version cutoffs.

basejump 0.14.16 (2021-03-02)

Minor changes:

  • Including additional reexports used in pointillism package.

basejump 0.14.17 (2021-03-12)

Minor changes:

  • Including useful stringr reexports that are used in a number of downstream packages.

basejump 0.14.18 (2021-05-18)

Minor changes:

  • Removed magrittr as an import, and removed magrittr pipes as reexports. Base R now supports native pipe in 4.1 release.

basejump 0.14.19 (2021-06-20)

Minor changes:

  • Updated median and quantile reexports to import from AcidGenerics instead of AcidBase. This now refers to median and quantile generics defined in IRanges package, which is useful for handling of NumericList objects.
  • Updated dependency version cutoffs.

basejump 0.14.20 (2021-08-04)

Minor changes:

  • Added simpleClass reexport from AcidBase package update.
  • Updated dependency package version cutoffs.

basejump 0.14.21 (2021-08-09)

Minor changes:

  • Updated dependency version cutoffs.
  • Removed mapEnsemblBuildToUCSC and mapUCSCBuildToEnsembl, which are no longer exported in the AcidGenomes package.

basejump 0.14.22 (2021-09-08)

New functions:

  • Added some reexports from AcidCLI: abort, inform, warn.

Removed functions:

  • Removed some deprecated functions: matchArgsToDoCall, matchEnsemblReleaseToURL, matchHumanOrthologs, matchesInterestingGroups, metadataBlacklist, multiassignAsEnvir, readSampleData, readTx2Gene, sortUnique, toStringUnique, and unlistToDataFrame.
  • Removed reexports from methods package: as, formalArgs, is, new, and validObject.

Minor changes:

  • Updated dependency version cutoffs.

basejump 0.14.23 (2021-09-13)

Minor changes:

  • Reworked method exports for aggregate and aggregateCols, following update in AcidSingleCell that improves the consistency of aggregate methods.
  • Updated dependency version cutoffs of other packages.