basejump 0.4.0 (2018-03-22)

Major changes

  • Introducing new functions for the acquistion of gene and transcript annotations from Ensembl: ensembl, genes, and transcripts. These functions allow the return of GRanges, DataFrame, and data.frame class objects from AnnotationHub using ensembldb.
  • Improved internal broadClass definition code to match against chromosome from Ensembl if available.
  • loadDataAsName now works with unquoted names, improving consistency with loadData (non-standard evaluation).

Minor changes

  • Added new convertUCSCBuildToEnsembl function, for easy remapping of UCSC to Ensembl genome build names (e.g. hg38 to GRCh38).
  • Migrated matrix methods for plotCorrelationHeatmap here from bcbioRNASeq, for improved consistency with other heatmap functions.
  • Exporting makeNames variant of base::make.names that sanitizes using underscores rather than dots.
  • Converted readYAML from a generic to standard function.
  • Added support for AppVeyor CI code testing on Windows.
  • Made Travis CI build checks stricter, adding support for BiocCheck.
  • Added new assert checks: assertAreGeneAnnotations, assertAreTranscriptAnnotations, isAnImplicitInteger.
  • Simplified working examples for assert checks to just show successes.

Deprecations

  • annotable function has been deprecated in favor of the new ensembl function.
  • checkAnnotable deprecated in favor of assertIsAnnotable.
  • checkGene2symbol deprecated in favor of assertIsGene2symbol.
  • checkTx2gene deprecated in favor of assertIsTx2gene.
  • assertFormalColorFunction deprecated in favor of assertIsHexColorFunctionOrNULL.
  • initializeDir deprecated in favor of initializeDirectory.
  • Defunct: summarizeRows, wash, packageSE, prepareSE, metadataTable, comp, revcomp, symbol2gene.

basejump 0.4.11 (2021-02-21)

Minor changes

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

basejump 0.4.12 (2021-02-22)

Minor changes

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

basejump 0.4.13 (2021-02-22)

Minor changes

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

basejump 0.4.14 (2021-02-24)

Minor changes

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

basejump 0.4.15 (2021-02-26)

Minor changes

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

basejump 0.4.16 (2021-03-02)

Minor changes

  • Including additional reexports used in pointillism package.

basejump 0.4.17 (2021-03-12)

Minor changes

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

basejump 0.4.18 (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 0.4.19 (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 0.4.22 (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.