systemPipeRdata: NGS 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.
Slide Shows
Installation
systemPipeRdata can be installed directly from GitHub using the devtools package from CRAN.
devtools::install_github("tgirke/systemPipeRdata")Alternatively, one can install it with the Bioconductor biocLite command.
source("http://bioconductor.org/biocLite.R")
biocLite("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 biocLite method as instructed here.
Usage
Detailed user manuals are available here:
Additional information can be found on the corresponding Bioconductor package overview page.
Material for Bioc2016 Tutorial
- Intro Slide Show
- Tutorial Material
Installation
Please install systemPipeRdata from this GitHub repository as shown below. This package provides the data and Rmd files for the tutorial.
Its parent package systemPipeR is a dependency and it should install along with all its own dependencies automatically. If it doesn't then please also
run the last biocLite install command given below.
source("http://bioconductor.org/biocLite.R")
biocLite("tgirke/systemPipeRdata", build_vignettes=TRUE, dependencies=TRUE)
biocLite("systemPipeR")