Version 1.2.4

• Change description of log fold change in help pages
• Change settings in simulation to matrix multiplication

Version 1.2.3

• Ensuring compability with R version 4.0
• Adapt log fold change model matrix addition
• Adapt methods of moments estimation of mean, dispersion and dropout during simulation
• Adding log fold changes to fraction of replicates per group (option p.G in Setup())

Version 1.1.0 relased

Version 1.1.0 released with the following changes / additions:

• 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