Changes in version 1.1.3 (2018-10-19)
========================

* Modified COR scores to reflect R^2 for regression on UV/WV/QC rather than max correlation.
* Bug fix for shiny report.
* Updated vignette.

Changes in version 1.1.2 (2017-7-3)
========================

* Moved many Imports: packages to Suggests: to reduce impact of loading scone

Changes in version 1.1.1 (2017-6-30)
========================

* Added fast ziber imputation method

Changes in version 1.0.0 (2017-4-6)
========================

* Faster SVD with rARPACK.
* New zero mode options in scone.
* Newly exported get functions.
* Updated scone scaling function defaults.
* Error handling and documentation updates.
* Bug fixes to sample filtering functions.

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.

Changes in version 0.0.8 (2016-09-26)
========================

* Added sconeReport() function for shiny browser of SCONE results.
* scone() outputs are now sorted according to mean *rank* of scores rather than mean scores. Although this is a relative measure it accounts for differing variability of metrics.
* RLE_IQR now quantifies the variability of the IQR RLE across samples, rather than the mean.
* Bug Fix: Previously imputation could be applied to the wrong subset of params rows when user passed params arguments. Imputation functions are now indexed by name to avoid this error.
* Bug Fix: Negative infinity expected likelihood is temporarily permitted in the ziber loop.
* "ezbake" script and scone_easybake() function added for pipelined SCONE commands.
* Revised documentation and removed old scripts.
* Various other bug fixes.

Changes in version 0.0.6 (2016-07-22)
========================

* Added option for restoring zeroes after scaling step.
* New argument format for imputation via impute_args.
* Simplified ziber fnr estimation function - requires control genes.
* Fixed bug when using plot functionality of filtering functions.
* "Conditional" pam replaced with "Stratified" pam, clustering each bio-cross-batch condition separately, rather than simply each bio condition.
* Simple FNR for filtering is now based on medians of natural log expression in "expressing" cells / robust to convergence issues.
* Removed all sufficient thresholds for metric sample filter.
* Added option to write normalized matrices to HDF5 file.
* Added wrapper function get_normalized() to retrieve normalized data.
* New biplot_interactive function to explore the results.

Changes in version 0.0.5
========================

* Modified biplot to handle general coloring schemes.
* Limit number of WV and UV factors to eval_pcs in computing WV and UV scores.
* Updated dependencies.
* Added error-handling to sample filter.
* Removed var preserved measure due to length of running time.

Changes in version 0.0.4
========================

* Fixed a few bugs and documentation mismatches.
* Removed stability evaluation (redundant with sil width and slow).
* Removed clusterExperiment dependency.
* Removed RUV correlation score. UV correlation now takes ruv control genes as default.
* Added RLE measures to scone evaluation.
* Added FQT_FN to implement careful ties handling by FQ.
* Better handling of plots in sample filter functions.
* Mean score rather than median rank to evaluate normalizations.
* Default value for imputation.
* Minor optimizations to evaluation functions.

Changes in version 0.0.3
========================

* Fixed various bugs.
* Added “compactness” measure for stability evaluation.
* Compute RUV factors only when needed.
* Fixed Github issues #11, #12, #13, #14, #21, #28.
* zinb now works for non-integer whole numbers.
* Updated tests.
* Added documentation for datasets.
* Added biplot_colored function.
