v0.99.0

@drisso drisso released this Nov 15, 2016 · 13 commits to master since this release

Changes in version 0.99.0 (2016-11-14)

  • Major release: many changes due to porting to S4.
  • Widespread updates to documentation, including examples.
  • Compatibility with Bioconductor format, including biocViews.
  • Updated cell-cycle genes.
  • Default BPPARAM value, now passed as argument to scone.
  • Removed zinb function.
  • Test different parallel back ends.
  • Added class SconeExperiment based on SummarizedExperiment.
  • Added constructor sconeExperiment to create SconeExperiment objects.
  • Added many helper methods to retrieve content of slots.
  • Wrapper get_normalized() to extract/compute single normalization from scone object.
  • Wrapper get_design() to extract the design matrix associated with a given normalization.
  • Method select_methods() to get a smaller SconeExperiment object containing only the requested normalization schemes.
  • biplot_interactive() now works with SconeExperiment objects.
  • Dropped date from DESCRIPTION as better practice is to add date to NEWS file.
  • Added wrapper for scran normalization, removed FQP.

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