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https://bvieth.github.io/powsimR/

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/

experimental-design gene-expression power power-analysis r rna-seq simulation simulation-framework single-cell

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Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

Lists

README 

        
---

output: github_document

---



```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```



# `powsimR` 
 Power analysis for bulk and 
 single cell RNA-seq experiments 



Please also consult my Github Page of [powsimR](https://bvieth.github.io/powsimR/) made with [pkgdown](http://pkgdown.r-lib.org/index.html)!



## :arrow_double_down: Installation Guide



For the installation, the R package `devtools` is needed.



```{r, echo=T, eval=F, tidy=T}

install.packages('devtools')

library(devtools)

```



I recommend to install first the dependencies manually and then powsimR. If you plan to use MAGIC for imputation, then please follow their [instruction](https://github.com/KrishnaswamyLab/MAGIC) to install the python implementation before installing powsimR.  



```{r, echo=T, eval=F, tidy=T}

ipak <- function(pkg, repository=c('CRAN', 'Bioconductor', 'github')){

  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]

  # new.pkg <- pkg

  if (length(new.pkg)) {

    if(repository=='CRAN') {

      install.packages(new.pkg, dependencies = TRUE)

    }

    if(repository=='Bioconductor') {

      if(strsplit(version[['version.string']], ' ')[[1]][3] > "4.0.0"){

        if (!requireNamespace("BiocManager")){

            install.packages("BiocManager")

        }

            BiocManager::install(new.pkg, dependencies=TRUE, ask=FALSE)

      }

      if(strsplit(version[['version.string']], ' ')[[1]][3] < "3.6.0"){

        stop(message("powsimR depends on packages and functions that are only available in R 4.0.0 and higher."))

      }

    }

    if(repository=='github') {

      devtools::install_github(new.pkg, build_vignettes = FALSE, force = FALSE, dependencies=TRUE)

    }

  }

}



# CRAN PACKAGES

cranpackages <- c("broom", "cobs", "cowplot", 

                  "data.table", "doParallel", "dplyr", "DrImpute", 

                  "fastICA", "fitdistrplus", "foreach", "future",

                  "gamlss.dist", "ggplot2", "ggpubr", "ggstance", "grDevices",

                  "grid", "Hmisc", "kernlab", "MASS", "magrittr", "MBESS", "Matrix",

                  "matrixStats", "mclust", "methods", "minpack.lm", "moments", "msir", 

                  "NBPSeq", "nonnest2", "parallel", "penalized", "plyr", "pscl",

                  "reshape2", "Rmagic", "rsvd", "Rtsne", "scales", "Seurat", "snow", "sctransform", 

                  "stats", "tibble", "tidyr", "truncnorm", "VGAM", "ZIM", "zoo")

ipak(cranpackages, repository='CRAN')



# BIOCONDUCTOR

biocpackages <- c("bayNorm", "baySeq", "BiocGenerics", "BiocParallel", 

                  "DESeq2", "EBSeq", "edgeR", "IHW", "iCOBRA",

                  "limma", "Linnorm", "MAST", "monocle", "NOISeq", "qvalue", "ROTS", "RUVSeq", 

                  "S4Vectors", "scater", "scDD", "scde", "scone", "scran", "SCnorm", 

                  "SingleCellExperiment", "SummarizedExperiment", "zinbwave")

ipak(biocpackages, repository='Bioconductor')



# GITHUB

githubpackages <- c('cz-ye/DECENT', 'nghiavtr/BPSC', 

                    'mohuangx/SAVER', 'statOmics/zingeR',

                    'Vivianstats/scImpute')

ipak(githubpackages, repository = 'github')

```



To check whether all dependencies are installed, you can run the following lines:



```{r depcheck, echo = TRUE, eval = FALSE, tidy = FALSE}



powsimRdeps <- data.frame(Package = c(cranpackages, 

                                      biocpackages, 

                                      sapply(strsplit(githubpackages, "/"), "[[", 2)), 

                          stringsAsFactors = F)



ip <- as.data.frame(installed.packages()[,c(1,3:4)], stringsAsFactors = F)



ip.check <- cbind(powsimRdeps, 

                  Version = ip[match(powsimRdeps$Package, rownames(ip)),"Version"]) 



table(is.na(ip.check$Version))  # all should be FALSE



```



After installing the dependencies, powsimR can be installed by using devtools as well.



```{r, echo=T, eval=F, tidy=T}

devtools::install_github('bvieth/powsimR', 

                         build_vignettes = TRUE, 

                         dependencies=FALSE)

library("powsimR")

```



Alternative, you can try to install powsimR and its dependencies directly using devtools:



```{r, echo=T, eval=F, tidy=T}

devtools::install_github("bvieth/powsimR")

```



## :book: User Guide



For examples and tips on using the package, please consult the vignette after successful installation by 



```{r, echo=T, eval=F, tidy=T}

browseVignettes('powsimR')

```



Some users have experienced issues installing powsimR due to vignette compilation errors or because they are missing the necessary R packages to build the vignette, i.e. knitr and rmdformats.  If that is the case, you can either install these dependencies or leave out building the vignette (by setting build_vignettes to FALSE) and read it on my Github Page of [powsimR](https://bvieth.github.io/powsimR/articles/powsimR.html) or download it as a html file [here](https://github.com/bvieth/powsimR/blob/master/vignettes/powsimR.html).



### DLLs and ulimit



Note that the error "maximal number of DLLs reached..." might occur due to the loading of many shared objects by Bioconductor packages. Restarting the R session after installing dependencies / powsimR will help.

Starting with R version 3.4.0, one can set the environmental variable 'R_MAX_NUM_DLLS' to a higher number. See `?Startup()` for more information. I recommend to increase the maximum number of DLLs that can be loaded to 500. The environmental variable R\_MAX\_NUM\_DLLS can be set in R\_HOME/etc/Renviron prior to starting R. For that locate the Renviron file and add the following line: R\_MAX\_NUM\_DLLS=xy where xy is the number of DLLs.

On my Ubuntu machine, the Renviron file is in /usr/lib/R/etc/ and I can set it to 500.



In addition, the user limits for open files (unix: ulimit) might have to be set to a higher number to accomodate the increase in DLLs. Please check out the help pages for [MACs](https://gist.github.com/tombigel/d503800a282fcadbee14b537735d202c) and [Linux](https://glassonionblog.wordpress.com/2013/01/27/increase-ulimit-and-file-descriptors-limit/) for guidance.



## :scroll: Citation



Please use the following entry for citing powsimR.



```{r, echo=T, eval=F, tidy=T}

citation("powsimR")

```



powsimR is published in [Bioinformatics](https://doi.org/10.1093/bioinformatics/btx435). 

A preprint paper is also on [bioRxiv](https://doi.org/10.1101/117150). 



## :incoming_envelope:  Notes



Please send bug reports and feature requests by opening a new issue on 

[this page](https://github.com/bvieth/powsimR/issues). 

I try to keep up to date with new developments / changes of methods implemented in powsimR, but if you encounter run errors while using a certain tool (e.g. for imputation), then I appreciate if you can post this as an [issue](https://github.com/bvieth/powsimR/issues).



## `R` Session Info



```{r}

library(powsimR)

sessionInfo()

```