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| # [mSigSDK](https://episphere.github.io/msig) | ||
| # mSigSDK: In-Browser Mutational Signature Analysis | ||
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| Mutational Signature SDK integrating the NCI [mSigPortal](https://analysistools-dev.cancer.gov/mutational-signatures/#/apiaccess) with the [ICGC Data Portal](https://dcc.icgc.org/) | ||
| ## Overview | ||
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| **mSigSDK** is a JavaScript Software Development Kit (SDK) designed to facilitate mutational signature analysis entirely within a web browser. Built to support research workflows involving mutational data, it interacts with APIs from [mSigPortal](https://analysistools.cancer.gov/mutational-signatures/) and adheres to modern web standards, ensuring compatibility, scalability, and privacy. | ||
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| This SDK allows researchers to analyze patient-specific genomic data without downloading sensitive information, providing a secure and private computational environment. With **mSigSDK**, researchers can: | ||
| - Visualize and compare mutational signatures. | ||
| - Perform dimensionality reduction, hierarchical clustering, and more. | ||
| - Extend functionality to other mutation signature ecosystems such as SIGNAL or COSMIC. | ||
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| --- | ||
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| ## Features | ||
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| - **In-Browser Computation**: All analyses are performed client-side using the user's computational resources. | ||
| - **Modular Design**: Adheres to ECMAScript ES6 standards, enabling easy integration and extension. | ||
| - **Visualizations**: Supports multiple interactive visualizations via Plotly and AMCharts. | ||
| - **APIs**: Seamlessly integrates with mSigPortal's REST APIs to fetch mutational signature data and metadata. | ||
| - **Data Privacy**: No data is sent to external servers; all operations are secure and local. | ||
| - **Extensibility**: Designed for interoperability with future APIs and datasets. | ||
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| --- | ||
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| ## Quick Start | ||
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| This is all you need to do to run mSigSDK. You don't need to install anything: | ||
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| 1. Navigate to any website that has not blocked module loading (e.g., [https://dceg.cancer.gov/](https://dceg.cancer.gov/)). | ||
| 2. Use `Fn + F12` to open your browser's developer console. | ||
| 3. Fetch the SDK by typing the following code into the console: | ||
| ```javascript | ||
| mSigSDK = (await import("https://episphere.github.io/msig/main.js")).mSigSDK | ||
| ``` | ||
| 4. Fetch some data from mSigPortal by typing the following code into the console: | ||
| ```javascript | ||
| data = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData() | ||
| ``` | ||
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| --- | ||
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| ## Development and Contributions | ||
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| ### Source Code | ||
| The source code is hosted on GitHub: [mSigSDK Repository](https://github.com/episphere/msig). | ||
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| ### Observable Notebooks | ||
| Explore interactive examples: [Observable Notebooks](https://observablehq.com/@aaronge-2020/signatures). | ||
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| ### Contact | ||
| **Aaron Ge** | ||
| Division of Cancer Epidemiology and Genetics, National Cancer Institute. | ||
| Email: [[email protected]](mailto:[email protected]). | ||
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| --- | ||
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| ## License | ||
| This project is open-source and available under the MIT license. |
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| <div id="main"> | ||
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| <h1 class="page-title">Home</h1> | ||
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| <h3> </h3> | ||
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| <h1 class="page-title">mSigSDK: In-Browser Mutational Signature Analysis</h1> | ||
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| <section> | ||
| <article><h1></h1> | ||
| <h2>Overview</h2> | ||
| <p><strong>mSigSDK</strong> is a JavaScript Software Development Kit (SDK) designed to facilitate mutational signature analysis entirely within a web browser. Built to support research workflows involving mutational data, it interacts with APIs from <a href="https://analysistools.cancer.gov/mutational-signatures/">mSigPortal</a> and adheres to modern web standards, ensuring compatibility, scalability, and privacy.</p> | ||
| <p>This SDK allows researchers to analyze patient-specific genomic data without downloading sensitive information, providing a secure and private computational environment. With <strong>mSigSDK</strong>, researchers can:</p> | ||
| <ul> | ||
| <li>Visualize and compare mutational signatures.</li> | ||
| <li>Perform dimensionality reduction, hierarchical clustering, and more.</li> | ||
| <li>Extend functionality to other mutation signature ecosystems such as SIGNAL or COSMIC.</li> | ||
| </ul> | ||
| <hr> | ||
| <h2>Features</h2> | ||
| <ul> | ||
| <li><strong>In-Browser Computation</strong>: All analyses are performed client-side using the user's computational resources.</li> | ||
| <li><strong>Modular Design</strong>: Adheres to ECMAScript ES6 standards, enabling easy integration and extension.</li> | ||
| <li><strong>Visualizations</strong>: Supports multiple interactive visualizations via Plotly and AMCharts.</li> | ||
| <li><strong>APIs</strong>: Seamlessly integrates with mSigPortal's REST APIs to fetch mutational signature data and metadata.</li> | ||
| <li><strong>Data Privacy</strong>: No data is sent to external servers; all operations are secure and local.</li> | ||
| <li><strong>Extensibility</strong>: Designed for interoperability with future APIs and datasets.</li> | ||
| </ul> | ||
| <hr> | ||
| <h2>Quick Start</h2> | ||
| <p>This is all you need to do to run mSigSDK. You don't need to install anything:</p> | ||
| <ol> | ||
| <li>Navigate to any website that has not blocked module loading (e.g., <a href="https://dceg.cancer.gov/">https://dceg.cancer.gov/</a>).</li> | ||
| <li>Use <code>Fn + F12</code> to open your browser's developer console.</li> | ||
| <li>Fetch the SDK by typing the following code into the console:<pre class="prettyprint source lang-javascript"><code>mSigSDK = (await import("https://episphere.github.io/msig/main.js")).mSigSDK | ||
| </code></pre> | ||
| </li> | ||
| <li>Fetch some data from mSigPortal by typing the following code into the console:<pre class="prettyprint source lang-javascript"><code>data = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData() | ||
| </code></pre> | ||
| </li> | ||
| </ol> | ||
| <hr> | ||
| <h2>Development and Contributions</h2> | ||
| <h3>Source Code</h3> | ||
| <p>The source code is hosted on GitHub: <a href="https://github.com/episphere/msig">mSigSDK Repository</a>.</p> | ||
| <h3>Observable Notebooks</h3> | ||
| <p>Explore interactive examples: <a href="https://observablehq.com/@aaronge-2020/signatures">Observable Notebooks</a>.</p> | ||
| <h3>Contact</h3> | ||
| <p><strong>Aaron Ge</strong><br> | ||
| Division of Cancer Epidemiology and Genetics, National Cancer Institute.<br> | ||
| Email: <a href="mailto:[email protected]">[email protected]</a>.</p> | ||
| <hr> | ||
| <h2>License</h2> | ||
| <p>This project is open-source and available under the MIT license.</p></article> | ||
| </section> | ||
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| <br class="clear"> | ||
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| <footer> | ||
| Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.4</a> on Fri Dec 27 2024 20:28:48 GMT-0500 (Eastern Standard Time) | ||
| Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 4.0.4</a> on Fri Dec 27 2024 20:41:26 GMT-0500 (Eastern Standard Time) | ||
| </footer> | ||
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| <script> prettyPrint(); </script> | ||
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