Example R analysis workflow

This is a makefile based R analysis workflow. Intermediate results are generated in incremental steps, with every analysis step corresponding to an (extension-less) file inside the script path.

The final output(s) is/are generated via a Knitr report. Together with intermediate data files (in the data path) and the figure files (in the report/figures/* paths), this represents the publishable output of the analysis.

The result can be previewed in report/report.html on the compiled branch.

To run the whole workflow, simply execute

make

on the command line.

This will first download the necessary raw data and then perform the analysis. Note that this will not install the required dependencies. Achieving this is an ongoing project.

Dependencies

Run on R v3.2.1.

This project has several package and several ‘box’ module dependencies:

Package dependencies

CRAN

• box
• ezknitr
• knitr
• readr
• tibble
• tidyr
• dplyr
• ggplot2

Bioconductor

• DESeq2 v1.8.2

Module dependencies

• klmr/sys@box-rewrite