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README.md
python3_notebook.ipynb
r_notebook.ipynb

README.md

Plugin Contribution Guide

Step-by-step guide illustrating how users can contribute RNA-seq analysis tools for integration into BioJupies (http://biojupies.cloud). Once integrated, the plugins are made available for notebook generation on the BioJupies website.

Overview

  1. What are BioJupies plugins?
  2. How do I submit a plugin?

What are BioJupies plugins?

BioJupies plugins are modular snippets of code which can analyze RNA-seq data and embed visualizations, interactive plots, or analysis results in Jupyter Notebooks.

Plugins may perform a variety of different analyses, ranging from exploratory data analysis visualizations, differential gene expression, clustering, enrichment analysis, and small molecule queries.

The full list of currently available plugins is available here.

How do I submit a plugin?

To submit your RNA-seq analysis tool as a plugin, follow the instructions below:

  1. Download one of the following files from the GitHub repository:

  2. Add your RNA-seq analysis code following the instructions in the notebook. The code should be divided into two functions:

    • An analyze function, which takes an RNA-seq dataset or gene signature as input, and returns the results of the analysis (e.g. as a dataframe, a list, or dictionary).
    • A plot function, which takes the output of the analyze function and displays by embedding a plot, table, or any type of interactive visualization in the notebook.
  3. Upload the notebook to GitHub. You can add the notebook to your personal GitHub repository, or create a new fork in the MaayanLab/biojupies-plugins repository.

  4. Fill the submission form on the BioJupies website: https://amp.pharm.mssm.edu/biojupies/contribute. You will be requested to specify a link to the notebook on GitHub, a contact email, and a brief description of the plugin.

  5. We will notify you on the status of the submission. Once completed, your plugin will be made available on the BioJupies website (http://biojupies.cloud) for Jupyter Notebook generation.

Contact Us

For more information or questions about submitting plugins, contact us at avi.maayan@mssm.edu or open an Issue on the GitHub repository.

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