hzongyao / systempiperdata

NGS workflow templates and sample data

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/systemPipeR", 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:

• systemPipeRdata Vignette
• systemPipeR Overview Vignette

Additional information can be found on the corresponding Bioconductor package overview page.