Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
@Divya1205
Divya1205 authored Aug 17, 2023
1 parent df49693 commit 1adc4c1
Showing 1 changed file with 12 additions and 229 deletions.
241 changes: 12 additions & 229 deletions README.md
View file
Original file line number Diff line number Diff line change
@@ -1,242 +1,25 @@
# RPCA_hotspot
<!-- Improved compatibility of back to top link: See: https://github.com/othneildrew/Best-README-Template/pull/73 -->
<a name="readme-top"></a>
<!--
*** Thanks for checking out the Best-README-Template. If you have a suggestion
*** that would make this better, please fork the repo and create a pull request
*** or simply open an issue with the tag "enhancement".
*** Don't forget to give the project a star!
*** Thanks again! Now go create something AMAZING! :D
-->


## Description:
Codes for the paper RBHS: https://doi.org/10.1002/prot.26047, a robust principal component analysis based method to predict preotein-protein interaction hot spots.

<!-- PROJECT SHIELDS -->
<!--
*** I'm using markdown "reference style" links for readability.
*** Reference links are enclosed in brackets [ ] instead of parentheses ( ).
*** See the bottom of this document for the declaration of the reference variables
*** for contributors-url, forks-url, etc. This is an optional, concise syntax you may use.
*** https://www.markdownguide.org/basic-syntax/#reference-style-links
-->
[![Contributors][contributors-shield]][contributors-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issues-shield]][issues-url]
[![MIT License][license-shield]][license-url]
[![LinkedIn][linkedin-shield]][linkedin-url]

## Background:
Proteins often exert their function by binding to other cellular partners. The hot spots are key residues for protein-protein binding. Their identification may shed light on the impact of disease associated mutations on protein complexes and help design protein-protein interaction inhibitors for therapy. Unfortunately, current machine learning methods to predict hot spots, suffer from limitations caused by gross errors in the data matrices. This has the codes for a novel data pre-processing pipeline that overcomes this problem by recovering a low rank matrix with reduced noise using Robust Principal Component Analysis. It further trains and validates machine learning classifiers to existing databases to show the predictive power of the method RBHS.



<h3 align="center">RBHS_Sitani</h3>

<p align="center">
Codes for the paper RBHS: https://doi.org/10.1002/prot.26047, a robust principal component analysis based method to predict preotein-protein interaction hot spots.
<br />
<a href="https://github.com/github_username/repo_name"><strong>Explore the docs »</strong></a>
<br />
<br />
<a href="https://github.com/github_username/repo_name">View Demo</a>
·
<a href="https://github.com/github_username/repo_name/issues">Report Bug</a>
·
<a href="https://github.com/github_username/repo_name/issues">Request Feature</a>
</p>
</div>
## Data provided:
train_HB34.xls is the file used for training the classifiers. It contains 313 rows indicating 313 interface residues and 59 columns, where 1-58 columns are features and column 59 is the label values.

test_BID18.xlsx is the independent test set file. It contains 126 rows indicating 126 interface residues and 59 columns, where 1-58 columns are features and column 59 is the label values.

## Environment file:

<!-- TABLE OF CONTENTS -->
<details>
<summary>Table of Contents</summary>
<ol>
<li>
<a href="#about-the-project">About The Project</a>
<ul>
<li><a href="#built-with">Built With</a></li>
</ul>
</li>
<li>
<a href="#getting-started">Getting Started</a>
<ul>
<li><a href="#prerequisites">Prerequisites</a></li>
<li><a href="#installation">Installation</a></li>
</ul>
</li>
<li><a href="#usage">Usage</a></li>
<li><a href="#roadmap">Roadmap</a></li>
<li><a href="#contributing">Contributing</a></li>
<li><a href="#license">License</a></li>
<li><a href="#contact">Contact</a></li>
<li><a href="#acknowledgments">Acknowledgments</a></li>
</ol>
</details>



<!-- ABOUT THE PROJECT -->
## About The Project

[![Product Name Screen Shot][product-screenshot]](https://example.com)

Here's a blank template to get started: To avoid retyping too much info. Do a search and replace with your text editor for the following: `github_username`, `repo_name`, `twitter_handle`, `linkedin_username`, `email_client`, `email`, `project_title`, `project_description`

<p align="right">(<a href="#readme-top">back to top</a>)</p>



### Built With

* [![Next][Next.js]][Next-url]
* [![React][React.js]][React-url]
* [![Vue][Vue.js]][Vue-url]
* [![Angular][Angular.io]][Angular-url]
* [![Svelte][Svelte.dev]][Svelte-url]
* [![Laravel][Laravel.com]][Laravel-url]
* [![Bootstrap][Bootstrap.com]][Bootstrap-url]
* [![JQuery][JQuery.com]][JQuery-url]

<p align="right">(<a href="#readme-top">back to top</a>)</p>



<!-- GETTING STARTED -->
## Getting Started

This is an example of how you may give instructions on setting up your project locally.
To get a local copy up and running follow these simple example steps.

### Prerequisites

This is an example of how to list things you need to use the software and how to install them.
* npm
```sh
npm install npm@latest -g
```

### Installation

1. Get a free API Key at [https://example.com](https://example.com)
2. Clone the repo
```sh
git clone https://github.com/github_username/repo_name.git
```
3. Install NPM packages
```sh
npm install
```
4. Enter your API in `config.js`
```js
const API_KEY = 'ENTER YOUR API';
```

<p align="right">(<a href="#readme-top">back to top</a>)</p>



<!-- USAGE EXAMPLES -->
## Usage

Use this space to show useful examples of how a project can be used. Additional screenshots, code examples and demos work well in this space. You may also link to more resources.

_For more examples, please refer to the [Documentation](https://example.com)_

<p align="right">(<a href="#readme-top">back to top</a>)</p>



<!-- ROADMAP -->
## Roadmap

- [ ] Feature 1
- [ ] Feature 2
- [ ] Feature 3
- [ ] Nested Feature

See the [open issues](https://github.com/github_username/repo_name/issues) for a full list of proposed features (and known issues).

<p align="right">(<a href="#readme-top">back to top</a>)</p>



<!-- CONTRIBUTING -->
## Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
Don't forget to give the project a star! Thanks again!
1. Fork the Project
2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)
3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)
4. Push to the Branch (`git push origin feature/AmazingFeature`)
5. Open a Pull Request
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- LICENSE -->
## License
Distributed under the MIT License. See `LICENSE.txt` for more information.
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- CONTACT -->
## Contact
Your Name - [@twitter_handle](https://twitter.com/twitter_handle) - email@email_client.com
Project Link: [https://github.com/github_username/repo_name](https://github.com/github_username/repo_name)
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- ACKNOWLEDGMENTS -->
## Acknowledgments
* []()
* []()
* []()
<p align="right">(<a href="#readme-top">back to top</a>)</p>
<!-- MARKDOWN LINKS & IMAGES -->
<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
[contributors-shield]: https://img.shields.io/github/contributors/github_username/repo_name.svg?style=for-the-badge
[contributors-url]: https://github.com/github_username/repo_name/graphs/contributors
[forks-shield]: https://img.shields.io/github/forks/github_username/repo_name.svg?style=for-the-badge
[forks-url]: https://github.com/github_username/repo_name/network/members
[stars-shield]: https://img.shields.io/github/stars/github_username/repo_name.svg?style=for-the-badge
[stars-url]: https://github.com/github_username/repo_name/stargazers
[issues-shield]: https://img.shields.io/github/issues/github_username/repo_name.svg?style=for-the-badge
[issues-url]: https://github.com/github_username/repo_name/issues
[license-shield]: https://img.shields.io/github/license/github_username/repo_name.svg?style=for-the-badge
[license-url]: https://github.com/github_username/repo_name/blob/master/LICENSE.txt
[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555
[linkedin-url]: https://linkedin.com/in/linkedin_username
[product-screenshot]: images/screenshot.png
[Next.js]: https://img.shields.io/badge/next.js-000000?style=for-the-badge&logo=nextdotjs&logoColor=white
[Next-url]: https://nextjs.org/
[React.js]: https://img.shields.io/badge/React-20232A?style=for-the-badge&logo=react&logoColor=61DAFB
[React-url]: https://reactjs.org/
[Vue.js]: https://img.shields.io/badge/Vue.js-35495E?style=for-the-badge&logo=vuedotjs&logoColor=4FC08D
[Vue-url]: https://vuejs.org/
[Angular.io]: https://img.shields.io/badge/Angular-DD0031?style=for-the-badge&logo=angular&logoColor=white
[Angular-url]: https://angular.io/
[Svelte.dev]: https://img.shields.io/badge/Svelte-4A4A55?style=for-the-badge&logo=svelte&logoColor=FF3E00
[Svelte-url]: https://svelte.dev/
[Laravel.com]: https://img.shields.io/badge/Laravel-FF2D20?style=for-the-badge&logo=laravel&logoColor=white
[Laravel-url]: https://laravel.com
[Bootstrap.com]: https://img.shields.io/badge/Bootstrap-563D7C?style=for-the-badge&logo=bootstrap&logoColor=white
[Bootstrap-url]: https://getbootstrap.com
[JQuery.com]: https://img.shields.io/badge/jQuery-0769AD?style=for-the-badge&logo=jquery&logoColor=white
[JQuery-url]: https://jquery.com
## Recommended software:
* Fiji or Napari
* If programming in Python, install scikit-image, opencv, Tensorflow, PyTorch
* If programming in MATLAB, install image processing toolbox

0 comments on commit 1adc4c1

Please sign in to comment.