initial commit

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 Elofsson Lab @ SciLifeLab 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

README.md

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+# 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.
+
+## 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

crosstalk.css

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+/* Adjust margins outwards, so column contents line up with the edges of the
+   parent of container-fluid. */
+.container-fluid.crosstalk-bscols {
+  margin-left: -30px;
+  margin-right: -30px;
+  white-space: normal;
+}
+
+/* But don't adjust the margins outwards if we're directly under the body,
+   i.e. we were the top-level of something at the console. */
+body > .container-fluid.crosstalk-bscols {
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
+  display: inline-block;
+  padding-right: 12px;
+  vertical-align: top;
+}
+
+@media only screen and (max-width:480px) {
+  .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
+    display: block;
+    padding-right: inherit;
+  }
+}