NEWS.md

In bvieth/powsimR: Power Simulations for RNA-sequencing

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()

bvieth/powsimR documentation built on Aug. 19, 2023, 7:48 p.m.