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NEWS.md

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Version 1.2.3 (2020-6-30)

  • Adapt methods of moments estimation of mean, dispersion and dropout during simulation.

Version 1.2.2 (2020-6-18)

  • Ensuring compability with R version 4.0 (e.g. deprecated DEDS Bioconductor package)
  • Adapt log fold change model matrix addition
  • Adding log fold changes to fraction of replicates per group (option p.G in Setup())

Version 1.2.0 (2019-7-30)

  • Downsampling of count matrices using binomial thinning implemented in estimateParam() (UMI-read ratio estimation) and simulateDE().
  • Setup of DE simulations now in one function (Setup()) instead of two.
  • estimateParam() with additional filtering options based on quality control checkup of scater package.
  • implement sctransform as a single cell normalisation method.

Version 1.1.3 (2018-07-10)

  • simulateDE() using SCnorm scaling factors as weights in limma-trend, limma-voom.

Version 1.1.2 (2018-06-20)

  • estimateParam() error fixed concerning expression cleanup.
  • precompiled vignette in inst/doc/.

Version 1.1.1 (2018-04-19)

  • simulateDE() now with the option to perform DE testing on filtered/imputed counts (option DEFilter)

Version 1.1.0 (2018-03-29)

  • simulation of batch effects (see options p.B, bLFC and bPattern in DESetup() and simulateCounts())
  • simulation of spike-in expression (see estimateSpike , plotSpike and option spikeIns in simulateDE and simulateCounts())
  • simulation of multiple sample groups (e.g. single cell populations) with simulateCounts()
  • imputation and prefiltering options prior to normalisation in DE power simulations added (scImpute, scone, Seurat, DrImpute, SAVER)
  • additional normalisation options and DE tools (esp. for single cells) included in simulateDE()
  • evaluation of simulation setup using estimated versus true value comparisons of library size factors and log2 fold changes in evaluateSim() and plotEvalSim()
  • increased flexibility in preprocessing for distribution evaluation in evaluateDist()