Package: powsimR
Type: Package
Title: Power Simulations for RNA-sequencing
Description: Recent development of very sensitive RNA-seq protocols, such as Smart-seq2 and CEL-seq allows transcriptional profiling at
               single-cell resolution and droplet devices make single cell transcriptomics high-throughput, allowing to characterize
               thousands or even millions of single cells. In powsimR, we have implemented a flexible tool to assess power and sample
               size requirements for differential expression (DE) analysis of single cell and bulk RNA-seq experiments. For our read
               count simulations, we (1) reliably model the mean, dispersion and dropout distributions as well as the relationship
               between those factors from the data. (2) Simulate read counts from the empirical mean-variance and dropout relations,
               while offering flexible choices of the number of differentially expressed genes, effect sizes and DE testing method. (3)
               Finally, we evaluate the power over various sample sizes. The number of replicates required to achieve the desired
               statistical power is mainly determined by technical noise and biological variability and both are considerably larger if
               the biological replicates are single cells. powsimR can not only estimate sample sizes necessary to achieve a certain
               power, but also informs about the power to detect DE in a data set at hand. We believe that this type of posterior
               analysis will become more and more important, if results from different studies are to be compared. Often enough
               researchers are left to wonder why there is a lack of overlap in DE-genes across similar experiments. PowsimR will allow
               the researcher to distinguish between actual discrepancies and incongruities due to lack of power.
Version: 1.2.5
Imports: bayNorm, baySeq, BiocGenerics, BiocParallel, broom, BPSC, cobs, cowplot, data.table, DECENT, DESeq2, doParallel, dplyr,
               DrImpute, EBSeq, edgeR, fastICA, fitdistrplus, foreach, future, ggplot2, ggpubr, ggstance, grDevices, grid, Hmisc,
               iCOBRA, IHW, kernlab, limma, Linnorm, magrittr, MASS, MAST, Matrix, matrixStats, methods, minpack.lm, moments, monocle,
               msir, NBPSeq, NOISeq, nonnest2, parallel, penalized, plotrix, plyr, pscl, qvalue, reshape2, rlang, Rmagic, ROTS, rsvd,
               Rtsne, RUVSeq, S4Vectors, SAVER, scales, scater, scDD, scde, SCnorm, scone, scran, sctransform, scuttle, Seurat,
               SingleCellExperiment, stats, SummarizedExperiment, tibble, tidyr, truncnorm, utils, VGAM, ZIM, zinbwave, zingeR, zoo
Remotes: nghiavtr/BPSC, cz-ye/DECENT, mohuangx/SAVER, rhondabacher/SCnorm, statOmics/zingeR, bioc::bayNorm, bioc::baySeq,
               bioc::BiocGenerics, bioc::BiocParallel, bioc::DESeq2, bioc::EBSeq, bioc::edgeR, bioc::iCOBRA, bioc::IHW, bioc::limma,
               bioc::Linnorm, bioc::MAST, bioc::monocle, bioc::NOISeq, bioc::qvalue, bioc::ROTS, bioc::RUVSeq, bioc::S4Vectors,
               bioc::scater, bioc::scDD, bioc::scde, bioc::scone, bioc::scran, bioc::scuttle, bioc::SingleCellExperiment,
               bioc::SummarizedExperiment, bioc::zinbwave
Depends: R (>= 4.0), gamlss.dist
Suggests: BiocStyle, knitr, rmdformats, mvtnorm, MBESS
LazyData: TRUE
Encoding: UTF-8
VignetteBuilder: knitr
License: GPL
NeedsCompilation: no
Author: Beate Vieth
Date: 2023-07-31
BugReports: https://github.com/bvieth/powsimR/issues
URL: https://github.com/bvieth/powsimR
Maintainer: Beate Vieth <vieth.beate@gmail.com>
RoxygenNote: 7.2.3
