basejump 0.13.0 (2020-10-05)

Migrated some functions to AcidBase, AcidGenomes, AcidPlyr, and pipette packages.

Major changes

  • Ensembl2Entrez: Improved internal matching engine, to allow reverse matching of Entrez identifiers to Ensembl identifiers.
  • Now exporting Entrez2Ensembl, which works like Entrez2Ensembl.
  • New S4 class Entrez2Ensembl, which inherits Ensembl2Entrez structure.

Minor changes

  • makeSummarizedExperiment: No longer requiring primary assay defined to be named “counts”. This isn’t appropriate for SummarizedExperiment objects defined in the new DepMapAnalysis package.
  • makeGRangesFromEnsembl: Include geneSynonyms column for supported organisms, including Homo sapiens.
  • Deprecated matchEnsemblReleaseToURL in favor of mapEnsemblReleaseToURL.

basejump 0.13.1 (2020-10-07)

Minor changes

  • Reworked makeSummarizedExperiment and makeSingleCellExperiment generators to generate empty objects without requiring any assays to be defined.

basejump 0.13.2 (2020-10-09)

Minor changes

  • Migrated transmit to pipette package. Still reexporting here.

basejump 0.13.3 (2020-11-24)

Minor changes

  • Updated dependency version cutoffs. Applies primarily to cli and magrittr.
  • Now rexporting new sem function from AcidBase.

basejump 0.13.4 (2020-12-04)

Minor changes

  • Added AsIs method support for sem, which is required for dplyr mutate calculations on numeric classes. Note that the numeric method is defined in the AcidBase package.