https://github.com/klmr/example-r-analysis

An example for an R analysis workflow using a Makefile, shell scripts and Knitr
https://github.com/klmr/example-r-analysis

Last synced: about 2 months ago
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An example for an R analysis workflow using a Makefile, shell scripts and Knitr

• Host: GitHub
• URL: https://github.com/klmr/example-r-analysis
• Owner: klmr
• License: other
• Created: 2016-09-09T16:29:59.000Z (about 8 years ago)
• Default Branch: main
• Last Pushed: 2021-07-10T15:18:43.000Z (about 3 years ago)
• Last Synced: 2024-06-11T08:48:12.811Z (4 months ago)
• Language: R
• Size: 28.3 KB
• Stars: 12
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• jimsghstars - klmr/example-r-analysis - An example for an R analysis workflow using a Makefile, shell scripts and Knitr (R)

README

        
# 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](http://htmlpreview.github.io/?https://github.com/klmr/example-r-analysis/blob/compiled/report/report.html).

To run the whole workflow, simply execute

```bash

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](https://github.com/klmr/box/milestone/4).

## 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](https://github.com/klmr/sys/commit/e7ebbef1fcd453704b16a31c6ed7f77d05800770)