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.

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.

Hotfix: 3D Plotting

Fixed plotting bug for 3d plots in sconeReport()

Release 0.0.8

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 estimate_ziber() loop.
• ezbake.R script and scone_easybake() function added for pipelined SCONE commands.
• Revised documentation and removed old scripts.
• Various other bug fixes.

Release 0.0.6

Changes in version 0.0.6

• 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.

Release 0.0.4

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 evaluations

Release 0.0.3

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