diff --git a/README.md b/README.md index b97f6d8..f9aea04 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,58 @@ -# [mSigSDK](https://episphere.github.io/msig) +# mSigSDK: In-Browser Mutational Signature Analysis -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 +**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. + +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. + +--- + +## Features + +- **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. + +--- + +## Quick Start + +This is all you need to do to run mSigSDK. You don't need to install anything: + +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() + ``` + +--- + +## Development and Contributions + +### Source Code +The source code is hosted on GitHub: [mSigSDK Repository](https://github.com/episphere/msig). + +### Observable Notebooks +Explore interactive examples: [Observable Notebooks](https://observablehq.com/@aaronge-2020/signatures). + +### Contact +**Aaron Ge** +Division of Cancer Epidemiology and Genetics, National Cancer Institute. +Email: [aaron.ge@nih.gov](mailto:aaron.ge@nih.gov). + +--- + +## License +This project is open-source and available under the MIT license. diff --git a/index.html b/index.html index 54ba083..05d0830 100644 --- a/index.html +++ b/index.html @@ -456,7 +456,7 @@

Try It Out

  • 3) Fetch the SDK by typing the following code into the console - 
    mSigSDK = (await import("https://episphere.github.io/msig/bundle.js")).mSigSDK
    + 
    mSigSDK = (await import("https://episphere.github.io/msig/main.js")).mSigSDK
     diff --git a/out/index.html b/out/index.html index 29f2f52..645ddc2 100644 --- a/out/index.html +++ b/out/index.html @@ -17,30 +17,59 @@
    -

    Home

    - - - - - - - - -

    - - - - - - - - - +

    mSigSDK: In-Browser Mutational Signature Analysis

    +
    +

    +

    Overview

    +

    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 and adheres to modern web standards, ensuring compatibility, scalability, and privacy.

    +

    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.
      • +
    +
    +

    Features

    +
      +
    • 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.
      • +
    +
    +

    Quick Start

    +

    This is all you need to do to run mSigSDK. You don't need to install anything:

    +
      +
    1. Navigate to any website that has not blocked module loading (e.g., https://dceg.cancer.gov/).
      2. +
    2. Use Fn + F12 to open your browser's developer console.
      3. +
    3. Fetch the SDK by typing the following code into the console:
      mSigSDK = (await import("https://episphere.github.io/msig/main.js")).mSigSDK
+
      +
      4. +
    4. Fetch some data from mSigPortal by typing the following code into the console:
      data = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData()
+
      +
      5. +
    +
    +

    Development and Contributions

    +

    Source Code

    +

    The source code is hosted on GitHub: mSigSDK Repository.

    +

    Observable Notebooks

    +

    Explore interactive examples: Observable Notebooks.

    +

    Contact

    +

    Aaron Ge
    +Division of Cancer Epidemiology and Genetics, National Cancer Institute.
    +Email: aaron.ge@nih.gov.

    +
    +

    License

    +

    This project is open-source and available under the MIT license.

    +
    @@ -56,7 +85,7 @@

    Home

    Namespaces