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: 3 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 (over 8 years ago)
- Default Branch: main
- Last Pushed: 2021-07-10T15:18:43.000Z (over 3 years ago)
- Last Synced: 2024-08-13T07:14:14.968Z (6 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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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)