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Version 0.2

AcidSingleCell 0.2.0 (2022-03-11)

Significantly reworked the package, migrating some single-cell RNA-seq analysis code that was previously defined in pointilllism package, but is generally applicable for any type of single-cell RNA-seq. We are reworking the pointillism package to function primarily as an extension toolkit for Seurat and monocle3.

New functions and classes:

  • Migrated barcodeRanksPerSample, cellCountsPerCluster, cpm, diffExp, diffExpPerCluster, findMarkers, and normalize methods that dispatch on SingleCellExperiment here from pointillism.
  • Migrated CellCycleMarkers, CellTypeMarkers, and KnownMarkers classes here from pointillism.

Major changes:

  • export: Reworked SingleCellExperiment method to support new BiocIO generic approach. This method functions similarly to SummarizedExperiment method, but also exports reducedDims matrices to disk as well.

Minor changes:

  • Multiple changes to NAMESPACE, reflecting migration of code from pointillism.
  • filterCells: Package metadata is now defined as "packageName" and "packageVersion", instead of previously using just "version".
  • Migrated KnownMarkers generic from here to AcidGenerics. Previously this was defined in pointillism package.