{"id":13683873,"url":"https://github.com/earmingol/cell2cell","last_synced_at":"2025-08-14T07:31:24.495Z","repository":{"id":39699822,"uuid":"182623687","full_name":"earmingol/cell2cell","owner":"earmingol","description":"User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting 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Inferring cell-cell interactions from transcriptomes with *cell2cell*\n[![PyPI Version][pb]][pypi]\n[![Documentation Status](https://readthedocs.org/projects/cell2cell/badge/?version=latest)](https://cell2cell.readthedocs.io/en/latest/?badge=latest)\n[![Downloads](https://pepy.tech/badge/cell2cell/month)](https://pepy.tech/project/cell2cell)\n\n\n[pb]: https://badge.fury.io/py/cell2cell.svg\n[pypi]: https://pypi.org/project/cell2cell/\n\n## :book: Getting started\nFor tutorials and documentation, visit [**cell2cell ReadTheDocs**](https://cell2cell.readthedocs.org/) or our [**cell2cell website**](https://earmingol.github.io/cell2cell).\n\n\n\n## :wrench: Installation\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cb\u003eStep 1: Install Anaconda\u003c/b\u003e :snake:\u003c/summary\u003e\n  \nFirst, [install Anaconda following this tutorial](https://docs.anaconda.com/anaconda/install/)\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cb\u003eStep 2: Create and Activate a New Conda Environment\u003c/b\u003e :computer:\u003c/summary\u003e\n\n```\n# Create a new conda environment\nconda create -n cell2cell -y python=3.7 jupyter\n\n# Activate the environment\nconda activate cell2cell\n```\n\u003c/details\u003e \n\n\u003cdetails\u003e \u003csummary\u003e\u003cb\u003eStep 3: Install cell2cell\u003c/b\u003e :arrow_down:\u003c/summary\u003e\n\n```\npip install cell2cell\n```\n\u003c/details\u003e\n\n## :bulb: Examples\n\n| cell2cell Examples | Tensor-cell2cell Examples |\n| --- | --- |\n| ![cell2cell Logo](https://github.com/earmingol/cell2cell/blob/master/Logo.png?raw=true) | ![Tensor-cell2cell Logo](https://github.com/earmingol/cell2cell/blob/master/LogoTensor.png?raw=true) |\n| - [Step-by-step Pipeline](https://github.com/earmingol/cell2cell/blob/master/examples/cell2cell/Toy-Example.ipynb)\u003cbr\u003e- [Interaction Pipeline for Bulk Data](https://earmingol.github.io/cell2cell/tutorials/Toy-Example-BulkPipeline)\u003cbr\u003e- [Interaction Pipeline for Single-Cell Data](https://earmingol.github.io/cell2cell/tutorials/Toy-Example-SingleCellPipeline)\u003cbr\u003e- [Whole Body of *C. elegans*](https://github.com/LewisLabUCSD/Celegans-cell2cell) | - [Obtaining patterns of cell-cell communication](https://earmingol.github.io/cell2cell/tutorials/ASD/01-Tensor-Factorization-ASD/)\u003cbr\u003e- [Downstream 1: Factor-specific analyses](https://earmingol.github.io/cell2cell/tutorials/ASD/02-Factor-Specific-ASD/)\u003cbr\u003e- [Downstream 2: Patterns to functions (GSEA)](https://earmingol.github.io/cell2cell/tutorials/ASD/03-GSEA-ASD/)\u003cbr\u003e- [Tensor-cell2cell in Google Colab (**GPU**)](https://colab.research.google.com/drive/1T6MUoxafTHYhjvenDbEtQoveIlHT2U6_?usp=sharing)\u003cbr\u003e- [Communication patterns in **Spatial Transcriptomics**](https://earmingol.github.io/cell2cell/tutorials/Tensor-cell2cell-Spatial/) |\n\nReproducible runs of the analyses in the [Tensor-cell2cell paper](https://doi.org/10.1038/s41467-022-31369-2) are available at [CodeOcean.com](https://doi.org/10.24433/CO.0051950.v2)\n\n## :link: LIANA \u0026 Tensor-cell2cell\n\nExplore our tutorials for using Tensor-cell2cell with [LIANA](https://github.com/saezlab/liana-py) at [ccc-protocols.readthedocs.io](https://ccc-protocols.readthedocs.io/).\n\n## :question: Common Issues\n\n- **Memory Errors with Tensor-cell2cell:** If you encounter memory errors when performing tensor factorizations, try replacing `init='svd'` with `init='random'`.\n  \n## :dna: Ligand-Receptor Pairs\nFind a curated list of ligand-receptor pairs for your analyses at our [GitHub Repository](https://github.com/LewisLabUCSD/Ligand-Receptor-Pairs).\n\n## :bookmark_tabs: Citation\n\nPlease cite our work using the following references:\n\n- **cell2cell**: [Inferring a spatial code of cell-cell interactions across a whole animal body](https://doi.org/10.1371/journal.pcbi.1010715).\n  *PLOS Computational Biology, 2022*\n\n- **Tensor-cell2cell**: [Context-aware deconvolution of cell-cell communication with Tensor-cell2cell](https://doi.org/10.1038/s41467-022-31369-2).\n  *Nature Communications, 2022.*\n\n- **LIANA \u0026 Tensor-cell2cell tutorials**: [Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples](https://doi.org/10.1016/j.crmeth.2024.100758).\n  *Cell Reports Methods, 2024*\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fearmingol%2Fcell2cell","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fearmingol%2Fcell2cell","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fearmingol%2Fcell2cell/lists"}