This pipeline is currently under development and does not have a stable release yet.
To obtain the systemPipeR and systemPipeRdata, please run as follow:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("systemPipeR")
BiocManager::install("systemPipeRdata")
To test workflows quickly or design new ones from existing templates, users can generate with a single command workflow instances fully populated with sample data and parameter files required for running a chosen workflow.
Use git or git-bash.exe (Windows) to download the template and run
git clone https://github.com/systemPipeR/SPclipseq.git
cd SPclipseq
To init the workflow management instance, run
library("systemPipeR")
sal <- SPRproject()
sal <- importWF(sal, file_path = "SPclipseq.Rmd")