From 1497f442a288adb8fdb9bc05b8cc979fcc7912f5 Mon Sep 17 00:00:00 2001 From: matteodelucchi Date: Wed, 10 Jul 2019 14:16:42 +0200 Subject: [PATCH] updated README --- README.md | 86 +------------------------------------------------------ 1 file changed, 1 insertion(+), 85 deletions(-) diff --git a/README.md b/README.md index 094ff18..e2712d6 100644 --- a/README.md +++ b/README.md @@ -1,90 +1,6 @@ # swissrepeat Collaboration with ZHAW on annotation and analysis of the SwissProt database in terms of tandem repeats and disorder. -The code is split in 1+3 parts. -It's started with the data collection, analysis and processing. -The other three parts are for the evaluation and exploration grouped into three Scripts: -swissrepeats.Rmd: which analyses the repeat data (analogous to marcotte et al.) -swissdisorder.Rmd: foo (TODO) -empirical_and_expected_homorepeat_counts.Rmd: foo (TODO) -ordered_and_disorderd_swissrepeats.Rmd: foo (TODO) -and finally: -manuscript_figures_and_data.Rmd: which contains the figures and data from the paper. +The results from the publication can be reproduced by running the scripts in `results/swissprot_*.Rmd`. -## Getting Started -These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system. - -### Prerequisites - -What things you need to install the software and how to install them - -``` -Give examples -``` - -### Installing -Make a copy of the ```local_config_TEMPLATE.R``` file by: -``` -cp local_config_TEMPLATE.R local_config.R -``` -In the newly created ```local_config.R``` specify system specific configurations. - -Install the required R-packages: -``` -install.packages(c("plyr", "pals", "ggplot2", "scales", "grid", "RColorBrewer", "tidyverse")) -``` - -## Running the tests - -Explain how to run the automated tests for this system - -### Break down into end to end tests - -Explain what these tests test and why - -``` -Give an example -``` - -### And coding style tests - -Explain what these tests test and why - -``` -Give an example -``` - -## Deployment - -Add additional notes about how to deploy this on a live system - -## Built With - -* [Dropwizard](http://www.dropwizard.io/1.0.2/docs/) - The web framework used -* [Maven](https://maven.apache.org/) - Dependency Management -* [ROME](https://rometools.github.io/rome/) - Used to generate RSS Feeds - -## Contributing - -Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c63ec426) for details on our code of conduct, and the process for submitting pull requests to us. - -## Versioning - -We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/your/project/tags). - -## Authors - -* **Billie Thompson** - *Initial work* - [PurpleBooth](https://github.com/PurpleBooth) - -See also the list of [contributors](https://github.com/your/project/contributors) who participated in this project. - -## License - -This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details - -## Acknowledgments - -* Hat tip to anyone whose code was used -* Inspiration -* etc