DESCRIPTION

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: 1.2.4
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, 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::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: 2020-11-30
BugReports: https://github.com/bvieth/powsimR/issues
URL: https://github.com/bvieth/powsimR
Maintainer: Beate Vieth <vieth.beate@gmail.com>
RoxygenNote: 7.1.1