Changes in version 1.17.1 (2021-07-21) o Improved PsiNorm vignette. o Fix bug that prevented PSINORM_FN() to be exported. Changes in version 1.15.1 (2021-05-06) o Add PsiNorm normalization method and its wrapper. o Add vignette that describes how to use PsiNorm. Changes in version 1.11.1 (2019-11-25) o Bug fix due to change in scran. Changes in version 1.9.2 (2019-10-07) o Change maintainer. o Fix tests. o Update vignette. Changes in version 1.1.3 (2018-10-19) o Modified COR scores to reflect R^2 for regression on UV/WV/QC rather than max correlation. o Bug fix for shiny report. o Updated vignette. Changes in version 1.1.2 o Moved many Imports: packages to Suggests: to reduce impact of loading scone Changes in version 1.1.1 o Added fast ziber imputation method Changes in version 1.0.0 o Faster SVD with rARPACK. o New zero mode options in scone. o Newly exported get functions. o Updated scone scaling function defaults. o Error handling and documentation updates. o Bug fixes to sample filtering functions. Changes in version 0.99.0 (2016-11-14) o Major release: many changes due to porting to S4. o Widespread updates to documentation, including examples. o Compatibility with Bioconductor format, including biocViews. o Updated cell-cycle genes. o Default BPPARAM value, now passed as argument to scone. o Removed zinb function. o Test different parallel back ends. o Added class SconeExperiment based on SummarizedExperiment. o Added constructor sconeExperiment to create SconeExperiment objects. o Added many helper methods to retrieve content of slots. o Wrapper get_normalized() to extract/compute single normalization from scone object. o Wrapper get_design() to extract the design matrix associated with a given normalization. o Method select_methods() to get a smaller SconeExperiment object containing only the requested normalization schemes. o biplot_interactive() now works with SconeExperiment objects. o Dropped date from DESCRIPTION as better practice is to add date to NEWS file. o Added wrapper for scran normalization, removed FQP. Changes in version 0.0.8 (2016-09-26) o Added sconeReport() function for shiny browser of SCONE results. o 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. o RLE_IQR now quantifies the variability of the IQR RLE across samples, rather than the mean. o 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. o Bug Fix: Negative infinity expected likelihood is temporarily permitted in the ziber loop. o "ezbake" script and scone_easybake() function added for pipelined SCONE commands. o Revised documentation and removed old scripts. o Various other bug fixes. Changes in version 0.0.6 (2016-07-22) o Added option for restoring zeroes after scaling step. o New argument format for imputation via impute_args. o Simplified ziber fnr estimation function - requires control genes. o Fixed bug when using plot functionality of filtering functions. o "Conditional" pam replaced with "Stratified" pam, clustering each bio-cross-batch condition separately, rather than simply each bio condition. o Simple FNR for filtering is now based on medians of natural log expression in "expressing" cells / robust to convergence issues. o Removed all sufficient thresholds for metric sample filter. o Added option to write normalized matrices to HDF5 file. o Added wrapper function get_normalized() to retrieve normalized data. o New biplot_interactive function to explore the results. Changes in version 0.0.5 o Modified biplot to handle general coloring schemes. o Limit number of WV and UV factors to eval_pcs in computing WV and UV scores. o Updated dependencies. o Added error-handling to sample filter. o Removed var preserved measure due to length of running time. Changes in version 0.0.4 o Fixed a few bugs and documentation mismatches. o Removed stability evaluation (redundant with sil width and slow). o Removed clusterExperiment dependency. o Removed RUV correlation score. UV correlation now takes ruv control genes as default. o Added RLE measures to scone evaluation. o Added FQT_FN to implement careful ties handling by FQ. o Better handling of plots in sample filter functions. o Mean score rather than median rank to evaluate normalizations. o Default value for imputation. o Minor optimizations to evaluation functions. Changes in version 0.0.3 o Fixed various bugs. o Added “compactness” measure for stability evaluation. o Compute RUV factors only when needed. o Fixed Github issues #11, #12, #13, #14, #21, #28. o zinb now works for non-integer whole numbers. o Updated tests. o Added documentation for datasets. o Added biplot_colored function.