Changes in version 1.30.0 (2024-10-30) o Minor maintenance chores: • Update roxygen2 version • Remove old CI config files • Add PR commands GitHub action • Re-configure pkgdown site • Add dependabot GitHub action • Update README Changes in version 1.28.0 (2024-05-01) o Properly prevent output from BASiCSEstimate() and scDDSimulate() when verbose = FALSE o Minor adjustments to tests to set verbose = FALSE and specify expected warnings o Replace the package man page with an auto-generated page o Add GitHub usernames and the Bioconductor package URL to description o Add @keywords internal and @noRd to function docs where needed o Modernise code by restyling using styler and fix other minor issues suggested by BiocCheck Changes in version 1.26.0 (2023-10-25) o Fixed a bug in splatSimPathDE() where DE factors were not adjusted based on the path origin (path.from parameter). This affected paths where the path origin was not the simulation origin (i.e. path.from != 0), particularly when the path DE was minimal. With this fix paths should no longer drift towards the origin. Changes in version 1.24.0 (2023-04-26) o Fixed bugs in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (from Christina Azodi) o Reduced core dependencies by importing scuttle rather than scater (scater is suggested) and making ggplot2 a suggested dependency. Changes in version 1.22.0 (2022-10-31) o Fixed a bug in BASiSSimulate() when spike.means is resampled o Fixed bugs in splatPopSimulate() with non-matching rownames and when sampling batches Changes in version 1.20.0 (2022-04-27) o The splatPop simulation is now published doi.org/10.1186/s13059-021-02546-1! o Improved initalisation of Params objects (from Wenjie Wang) o Improved fitting of dropout in splatEstimate() • Better initialisation of fitting as suggested by the InferCNV package • Additional fallback method o Bug fixes for the splat simulation o Bug fixes for the the splatPop simulation (from Christina Azodi) Changes in version 1.18.0 (2021-10-27) o Updates to the splatPop simulation (from Christina Azodi) • Added functionality to simulate directly from empirical values • Added eqtl.coreg parameter to splatPop • Fixed a bug where too many cells were simulated in splatPop with multiple batches • Fixed duplicate cell names in splatPopSimulate o Improved checks for group.prob in SplatParams o Automatically rescale group.prob during setting if it doesn't sum to 1 Changes in version 1.16.0 (2021-05-20) o Substantial updates to the splatPop simulation (from Christina Azodi) • Added ability to simulate data with complex multiplexed sequencing designs • Added simulation of “conditional” effects, where a subset of DE and eQTL effects are applied to only a subset of individuals (e.g. disease vs. healthy samples) • Added the ability to simulate different numbers of cells for each sample, sampled from a gamma distribution. • Updates to the splatPop vignette describing these changes o Logical matrices should now be handled correctly when minimising output SingleCellExperiment objects o Other minor fixes Changes in version 1.14.0 (2020-10-28) o Add the splatPop simulation. This is a extension to the splat simulation contributed by Christina Azodi and Davis McCarthy that adds population effects. It allows you to specify relatedness between individuals and generate cell-type specific eQTL effects. o Add a batch.rmEffect parameter to the Splat simulation. This allows generation of a paired simulation without any batch effects. o Add a new minimiseSCE function which can be used to remove unneeded information from simulation output (or any SingleCellExperiment) o All simulations now return sparse assay matrices by default when they would be smaller than the equivalent dense matrix. This is controlled by a new sparsify argument. o Users will now be automatically prompted to install packages if they try to use a simulation for which the suggested dependencies are not available Changes in version 1.12.0 (2020-04-20) o Add checks for cycles in the Splat path.from parameter. o Use alternative algorithm if fitting dropout fails in splatEstimate. o Adjust paths example in vignette. o Replace defunct functions in vignettes. o Minor fixes for compatibility with updates to other packages. Changes in version 1.10.0 (2019-10-20) o Add the (experimental) Kersplat simulation model. This model incorporates a gene network and other useful features. o Refactor the summariseDiff function and add the KS statistic. o Add variable gene correlation plot to compareSCEs and violins to other comparison plots. o Check for counts assay when estimating from SingleCellExperiment objects. o Fix where simpleSimulate stores parameters. o Fix bugs where parameters were not being passed correctly in BASiCSEstimate and sparseDCEstimate. o Replace the sc_example_counts dataset from scater with the mockSCE function. o Tidy and improve estimation function examples and add checks for suggested packages. o Various fixes for compatibility with updates to other packages. Changes in version 1.8.0 (2019-04-18) o Add a Splat parameters vignette o Rename the Splat path.length parameter to path.nSteps o Fix a bug with parameter order in setParams o Fix a bug where Splat groups were being simulated in alphanumeric order o Protect against integer overflow in simulation functions Changes in version 1.6.0 (2018-10-29) o Fix bug and improve normality testing in splatEstLib o Fixes for compatibility with the latest version of BASiCS, BASiCSEstimate now uses the regression method o Fix bug in getLNormFactors when reversing factors less than one o Various updates to tests and documentation Changes in version 1.3.5 (2018-04-25) o Move scater to Imports and add scater version o Remove lingering references to SCESets o Add option to use a normal distribution for library sizes in Splat simulations o Allow Splat dropout parameters to be specified by experiment, batch, group or cell o Add SparseDC simulation o Rename params in metadata slot of simulation to Params for consistency o Improve and colourise Params print output o Improve test coverage o Various other minor updates and bug fixes Changes in version 1.1.8 (2017-10-13) o Now published in Genome Biology! o Converted to the SingleCellExperiment object o Added new simulations: BASiCS, mfa, PhenoPath, ZINB-WaVE o Added batch effects to the Splat simulation. This required a change to the SplatParams object. o Improved scDD estimation o Added and improved comparison functions o Improved default Splat parameters and estimation o Improvements to the Lun2Params object o Added addGeneLength function o Updated simulation references o Various other minor updates and bug fixes Changes in version 0.99.16 (2017-04-23) o Splatter is a package for the simple simulation of single-cell RNA-seq data, including: o Multiple simulation models o Parameter estimation from real data o Functions for comparing simulations and real datasets o Simulation of complex groups and differentiation paths Changes in version 0.99.0 (2016-12-05) o Package prepared for Bioconductor submission.