Welcome to FUNKI

Welcome to FUNKI, the omics FUNctional analysis worKflows Interface tool. This Python package is intended to integrate different omic data analysis workflows including a graphical user interface (GUI), but also as a standalone Python package that users can integrate into their existing pipelines.

Disclaimer

This package is currently in development and features are being added regularly. If you have any ideas/suggestions or if you find any bug, please feel free to open an GitHub issue. You can also contribute via pull request.

This package is being developed by Nicolàs Palacio-Escat based on previous work from Hanna Schumacher and Rosa Hernansaiz-Ballesteros as part of the Saezlab, Institute for Computational Biomedicine, Univeristy Hospital Heidelberg.

This work is being funded by the CRC 1550 - Molecular Circuits of Heart Disease.

Installation

To install FUNKI in your local computer you can use pip as follows:

pip install git+https://github.com/saezlab/funki

Usage

Everything within FUNKI is works around an instance of a DataSet object. This class in turn inherits (i.e. is built on top of) the anndata.AnnData class. You can explore all implemented functionalities available programmatically in the Documentation.

If you want to access FUNKI via the GUI, you need to execute the application script with your Python interpreter, but first you need to download and install FUNKI using the commands below:

git clone git@github.com:saezlab/FUNKI.git
cd FUNKI
pip install ./

Now you can launch the FUNKI by simply running the application script:

python src/funki/app.py

This should automatically open the application in your default internet browser. If that is not the case, you can type or copy the following address (default) in the browser bar: http://127.0.0.1:8050/

Note: Refreshing the browser page will also restart the application.

Documentation

You can find the full documentation here, in the FUNKI documentation webpage.

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Developed by Nicolàs Palacio-Escat - Saezlab 2024