Note: the most recent version of this tutorial can be found here.
Note: if you use
systemPipeR in published research, please cite:
Backman, T.W.H and Girke, T. (2016).
systemPipeR: NGS Workflow and Report Generation Environment. BMC Bioinformatics, 17: 388. 10.1186/s12859-016-1241-0.
The intended way of running
systemPipeR workflows is via
*.Rmd files, which
can be executed either line-wise in interactive mode or with a single command from
R or the command-line. This way comprehensive and reproducible analysis reports
can be generated in PDF or HTML format in a fully automated manner by making use
of the highly functional reporting utilities available for R.
Templates for setting up custom project reports are provided as
by the helper package
systemPipeRdata and in the vignettes subdirectory of
systemPipeR. The corresponding HTML of these report templates are available here:
systemPipeVARseq. To work with
*.Rmd files efficiently, basic knowledge of
R Markdown v2 is required.