basejump 0.12.0 (2020-01-20)

Major changes

  • Migrated functions from brio (now renamed to pipette), freerange, and transformer, in preparation for Bioconductor submission and reviews.
  • Updated messages to utilize the cli package.

basejump 0.12.1 (2020-01-30)

Major changes

  • Reworked aggregate, aggregateCols, aggregateRows support to reflect internal migration away from Matrix.utils dependency.

Minor changes

  • NAMESPACE fix for unexpected removal of Matrix.utils from CRAN. Now defining the previously imported aggregate.Matrix function directly here in basejump.
  • aggregate: Now defining matrix method.
  • aggregate* generics now consistently use “x” instead of “object”.

basejump 0.12.2 (2020-02-18)

Minor changes

  • Migrating pseudobulk methods to pointillism package. Rethinking the approach used here to work better with per-cluster aggregation operations. Will be updated in the next pointillism release.

basejump 0.12.3 (2020-02-24)

Minor changes

  • makeSingleCellExperiment, makeSummarizedExperiment: Removed spikeNames support due to a breaking change in SingleCellExperiment, which has removed isSpike in favor of altExps. Refer to the SingleCellExperiment documentation for updated current best practice for handling spike-in transcripts, which now requires slotting a separate SummarizedExperiment object containing things like ERCCs inside the main SingleCellExperiment.