systemPipeRdata: Workflow templates and sample data
systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq, Ribo-Seq and many others.
Installation
To install the package, please use the BiocManager::install command:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("systemPipeRdata")
To obtain the most recent updates immediately, one can install it directly from github as follow:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("tgirke/systemPipeRdata", build_vignettes=TRUE, dependencies=TRUE)
Due to the large size of the sample data (~320 MB) provided by systemPipeRdata, its download/install may take some time.
To install the parent package systemPipeR itself, please use the BiocManager::install method as instructed here.
Usage
Detailed user manuals are available here:
Additional information can be found on the corresponding Bioconductor packages.