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| # swissrepeat | ||
| Collaboration with ZHAW on annotation and analysis of the SwissProt database in terms of tandem repeats and disorder. | ||
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| 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`. | ||
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| ## Getting Started | ||
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| 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. | ||
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| ### Prerequisites | ||
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| What things you need to install the software and how to install them | ||
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| ``` | ||
| Give examples | ||
| ``` | ||
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| ### 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. | ||
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| Install the required R-packages: | ||
| ``` | ||
| install.packages(c("plyr", "pals", "ggplot2", "scales", "grid", "RColorBrewer", "tidyverse")) | ||
| ``` | ||
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| ## Running the tests | ||
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| Explain how to run the automated tests for this system | ||
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| ### Break down into end to end tests | ||
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| Explain what these tests test and why | ||
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| ``` | ||
| Give an example | ||
| ``` | ||
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| ### And coding style tests | ||
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| Explain what these tests test and why | ||
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| ``` | ||
| Give an example | ||
| ``` | ||
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| ## Deployment | ||
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| Add additional notes about how to deploy this on a live system | ||
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| ## Built With | ||
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| * [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 | ||
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| ## Contributing | ||
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| 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. | ||
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| ## Versioning | ||
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| We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/your/project/tags). | ||
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| ## Authors | ||
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| * **Billie Thompson** - *Initial work* - [PurpleBooth](https://github.com/PurpleBooth) | ||
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| See also the list of [contributors](https://github.com/your/project/contributors) who participated in this project. | ||
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| ## License | ||
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| This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details | ||
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| ## Acknowledgments | ||
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| * Hat tip to anyone whose code was used | ||
| * Inspiration | ||
| * etc |