v0.99.0

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.