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.