cell2cell
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
BSD-3-CLAUSE License
Inferring cell-cell interactions from transcriptomes with cell2cell
📖 Getting started
For tutorials and documentation, visit cell2cell ReadTheDocs or our cell2cell website.
🔧 Installation
First, install Anaconda following this tutorial
# Create a new conda environment
conda create -n cell2cell -y python=3.7 jupyter
# Activate the environment
conda activate cell2cell
pip install cell2cell
💡 Examples
Reproducible runs of the analyses in the Tensor-cell2cell paper are available at CodeOcean.com
🔗 LIANA & Tensor-cell2cell
Explore our tutorials for using Tensor-cell2cell with LIANA at ccc-protocols.readthedocs.io.
❓ Common Issues
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Memory Errors with Tensor-cell2cell: If you encounter memory errors when performing tensor factorizations, try replacing
init='svd'withinit='random'.
🧬 Ligand-Receptor Pairs
Find a curated list of ligand-receptor pairs for your analyses at our GitHub Repository.
📑 Citation
Please cite our work using the following references:
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cell2cell: Inferring a spatial code of cell-cell interactions across a whole animal body. PLOS Computational Biology, 2022
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Tensor-cell2cell: Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nature Communications, 2022.
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LIANA & Tensor-cell2cell tutorials: Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. Cell Reports Methods, 2024
