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https://github.com/earmingol/sccellfie

scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.
https://github.com/earmingol/sccellfie

metabolic-modeling metabolic-pathways metabolism single-cell single-cell-transcriptomics spatial-transcriptomics systems-biology

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scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.

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.. |PYPI| image:: https://badge.fury.io/py/sccellfie.svg

   :target: https://pypi.org/project/sccellfie/



.. |Issues| image:: https://github.com/earmingol/scCellFie/actions/workflows/tests.yml/badge.svg

   :alt: test-sccellfie



.. |Codecov| image:: https://codecov.io/gh/earmingol/scCellFie/graph/badge.svg?token=22NENAKNKI

   :target: https://codecov.io/gh/earmingol/scCellFie



.. |Downloads| image:: https://pepy.tech/badge/sccellfie/month

   :target: https://pepy.tech/project/sccellfie



Metabolic activity from single-cell and spatial transcriptomics with scCellFie

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scCellFie is a computational tool for studying metabolic tasks using Python, inspired by the original implementation of

`CellFie `_, another tool originally developed in MATLAB by the `Lewis Lab `_. This version is designed to be

compatible with single-cell and spatial data analysis using Scanpy, while including a series of improvements and new analyses.



.. image:: https://github.com/earmingol/scCellFie/blob/main/scCellFie-Logo.png?raw=true

   :alt: Logo

   :width: 350

   :height: 188.31

   :align: center



Installation

------------



To install scCellFie, use pip::



    pip install sccellfie



Features

--------



- **Single cell and spatial data analysis:** Tailored for analysis of metabolic

  tasks using fully single cell resolution and in space.



- **Speed:** This implementation further leverages the original CellFie. It is now memory

  efficient and run much faster! A dataset of ~70k single cells can be analyzed in ~5 min.



- **New analyses:** From marker selection of relevant metabolic tasks to integration with

  inference of cell-cell communication.



- **User-friendly:** Python-based for easier use and integration into existing workflows.



- **Scanpy compatibility:** Fully integrated with Scanpy, the popular single cell

  analysis toolkit.



- **Organisms:** Metabolic database and analysis available for human and mouse.



How to cite

-----------



*Preprint is coming soon!*



Acknowledgments

---------------



This implementation is inspired by the original `CellFie tool `_ developed by

the `Lewis Lab `_. Please consider citing their work if you find this tool useful:



- **Model-based assessment of mammalian cell metabolic functionalities using omics data**.

  *Cell Reports Methods, 2021*. https://doi.org/10.1016/j.crmeth.2021.100040



- **ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data**.

  *STAR Protocols, 2023*. https://doi.org/10.1016/j.xpro.2023.102069



- **Inferring secretory and metabolic pathway activity from omic data with secCellFie**.

  *Metabolic Engineering, 2024*. https://doi.org/10.1016/j.ymben.2023.12.006