Bioconductor 3.19

• Properly prevent output from BASiCSEstimate() and scDDSimulate() when verbose = FALSE
• Minor adjustments to tests to set verbose = FALSE and specify expected warnings
• Replace the package man page with an auto-generated page
• Add GitHub usernames and the Bioconductor package URL to DESCRIPTION
• Add @keywords internal and @noRd to function docs where needed
• Modernise code by restyling using styler and fix other minor issues suggested by BiocCheck()

Full Changelog: v1.26.0...v1.28.0

Bioconductor 3.18

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.

Full Changelog: v1.24.0...v1.26.0

Bioconductor 3.17

• Fixed bugs in splatPopSimulate() where conditional group assignments were incorrect when batch effects were applied (PR #161 @azodichr, fixes #158, fixes #160)
• Replace all uses of set.seed with withr::with_seed() (@lazappi)
• Reduced core dependencies by importing scuttle rather than scater (scater is suggested) and making ggplot2 a suggested dependency (@lazappi , fixes #75)

Full Changelog: v1.22.0...v1.24.0

Bioconductor 3.16

• Fixed a bug in BASiCSSimulate() when spike.means is resampled (Fixes #153)
• Fixed bugs in splatPopSimulate() with non-matching rownames and when sampling batches (PR #151 @azodichr, fixes #149)

Full Changelog: v1.20.0...v1.22.0

Bioconductor 3.15

• The splatPop simulation is now published in Genome Biology 🎉 ! (Fixes #128, PR #129 @azodichr)
• Improved initialisation of Params objects (Fixes #132, PR #134 @wenjie2wang)
• Improved fitting of dropout in splatEstimate()
  • Better initialisation of fitting as suggested by the InferCNV package (Fixes #142)
  • Additional fallback method (Fixes #133)
• Bug fixes for the splat simulation
  • Replace scran::computeSumFactors() with scuttle::pooledSizeFactors() in lun2Estimate() (Fixes #130)
  • Removed duplicated code in splatSimPathCellMeans() (Fixes #131)
• Bug fixes for the the splatPop simulation
  • • Fixed bug where conditional eQTL effects were being incorrectly allocated (Fixes #125, @azodichr)

Full Changelog: v1.18.0...v1.20.0

Bioconductor 3.14

• Updates to the splatPop simulation (from @azodichr)
  • 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 (#118)
• Improved checks for group.prob in SplatParams (#107)
  • Automatically rescale group.prob during setting if it doesn't sum to 1

Full Changelog: v1.16.0...v1.18.0

Bioconductor 3.13

• Substantial updates to the splatPop simulation (from @azodichr)
  • 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
• Logical matrices should now be handled correctly when minimising output SingleCellExperiment objects
• Other minor fixes

Bioconductor 3.12

• Add the splatPop simulation. This is a extension to the splat simulation contributed by @azodichr and @davismcc that adds population effects. It allows you to specify relatedness between individuals and generate cell-type specific eQTL effects. (PR #106)
• Add a batch.rmEffect parameter to the Splat simulation. This allows generation of a paired simulation without any batch effects. (From @daynefiler PR #103)
• Add a new minimiseSCE() function which can be used to remove unneeded information from simulation output (or any SingleCellExperiment).
• 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.
• Users will now be automatically prompted to install packages if they try to use a simulation for which the suggested dependencies are not available.

Bioconductor 3.11

• Add checks for cycles in the Splat path.from parameter.
• Use alternative algorithm if fitting dropout fails in splatEstimate().
• Adjust paths example in vignette.
• Replace defunct functions in vignettes.
• Minor fixes for compatibility with updates to other packages.

Bioconductor 3.10

• Add the (experimental) Kersplat simulation model. This model incorporates a gene network and other useful features.
• Refactor the summariseDiff() function and add the KS statistic.
• Add variable gene correlation plot to compareSCEs() and violins to other comparison plots.
• Check for counts assay when estimating from SingleCellExperiment objects.
• Fix where simpleSimulate() stores parameters.
• Fix bugs where parameters were not being passed correctly in BASiCSEstimate() and sparseDCEstimate().
• Replace the sc_example_counts dataset from scater with the mockSCE() function.
• Tidy and improve estimation function examples and add checks for suggested packages.
• Various fixes for compatibility with updates to other packages.