systemPipeR 2.10.0
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 *.Rmd files
by the helper package systemPipeRdata and in the vignettes subdirectory of
systemPipeR. The corresponding HTML of these report templates are available here: systemPipeRNAseq, systemPipeRIBOseq, systemPipeChIPseq and systemPipeVARseq. To work with *.Rmd files efficiently, basic knowledge of knitr and Latex or R Markdown v2 is required.