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.
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.
Everything within FUNKI is works around an instance of a
DataSet
class. This object inherits (i.e. is built on top of) the
anndata.AnnData
class. If you are not familiar with this data structure, you can read more about it their
publication or explore
the package documentation.
To install FUNKI in your local computer you can use pip as follows:
pip install git+https://github.com/saezlab/funkiYou can also install it by cloning or downloading the code in this repository as described below.
If you want to access FUNKI via the graphical interface, you can download the executable here. If there is no executable build for your OS, you can also execute the application script with the Python interpreter as follows:
First you need to download and install FUNKI using the commands below:
git clone [email protected]:saezlab/FUNKI.git
cd FUNKI
pip install ./Now you can launch the FUNKI interface by simply executing the application script with:
python src/funki/app/main.pyYou can explore all implemented functionalities available programmatically in the Documentation.
For GUI usage, you can explore the help pages within the application's "Help" menu.
Developed by Nicolàs Palacio-Escat - Saezlab 2025