NEWS

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scone 1.17.1 (2021-07-21)

• Improved PsiNorm vignette.
• Fix bug that prevented PSINORM_FN() to be exported.

scone 1.15.1 (2021-05-06)

• Add PsiNorm normalization method and its wrapper.
• Add vignette that describes how to use PsiNorm.

scone 1.11.1 (2019-11-25)

• Bug fix due to change in scran.

scone 1.9.2 (2019-10-07)

• Change maintainer.
• Fix tests.
• Update vignette.

scone 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.

scone 1.1.2

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

scone 1.1.1

• Added fast ziber imputation method

scone 1.0.0

• 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.

scone 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.

scone 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.

scone 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.

scone 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.

scone 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.

scone 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.