Inferring cell-cell interactions from transcriptomes with cell2cell

:book: Getting started

For tutorials and documentation, visit cell2cell ReadTheDocs or our cell2cell website.

Step 1: Install Anaconda :snake:

Step 2: Create and Activate a New Conda Environment :computer:

# Create a new conda environment
conda create -n cell2cell -y python=3.7 jupyter

# Activate the environment
conda activate cell2cell

Step 3: Install cell2cell :arrow_down:

pip install cell2cell

cell2cell Examples	Tensor-cell2cell Examples

- Step-by-step Pipeline - Interaction Pipeline for Bulk Data - Interaction Pipeline for Single-Cell Data - Whole Body of C. elegans - Identifying a spatial code of ligand-receptor pairs (Genetic Algorithm) - Reproducing the C. elegans spatial code - Customizing the objective function	- Obtaining patterns of cell-cell communication - Downstream 1: Factor-specific analyses - Downstream 2: Patterns to functions (GSEA) - Tensor-cell2cell in Google Colab (GPU) - Communication patterns in Spatial Transcriptomics - Multi-modal communication patterns with Coupled Tensor Component Analysis

Reproducible runs of the analyses in the Tensor-cell2cell paper are available at CodeOcean.com

Explore our tutorials for using Tensor-cell2cell with LIANA at ccc-protocols.readthedocs.io.

Memory Errors with Tensor-cell2cell: If you encounter memory errors when performing tensor factorizations, try replacing init='svd' with init='random'.

Find a curated list of ligand-receptor pairs for your analyses at our GitHub Repository.

Please cite our work using the following references:

cell2cell: Inferring a spatial code of cell-cell interactions across a whole animal body. PLOS Computational Biology, 2022
Tensor-cell2cell: Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nature Communications, 2022.
Tensor-cell2cell v2: Tensor-cell2cell v2 unravels coordinated dynamics of protein- and metabolite-mediated cell-cell communication. Bioinformatics, 2026.
LIANA & Tensor-cell2cell tutorials: Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. Cell Reports Methods, 2024

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution for cell2cell 0.9.0
File	Size	Uploaded
cell2cell-0.9.0.tar.gz	252.5 kB	Sep 2, 2026	Details

Table of built distributions (wheels) for cell2cell 0.9.0
File	Interpreter	ABI	Platform	Reset
cell2cell-0.9.0-py3-none-any.whl 213.8 kB Sep 2, 2026	Python 3	none	any	Details

Total release size: 466.3 kB

Download URL	cell2cell-0.9.0.tar.gz
Size	252.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`81a8f7c7ec018bdf4584a004f822c6fa44817e4b2f79b4c392fae7ee94326e46`
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Upload date	Sep 2, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.9.25`

Download URL	cell2cell-0.9.0-py3-none-any.whl
Size	213.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`4a2d2e3cfb7706def00183fe8205ae08a1106bf166b33ea6c23d9b842098f4d6`
BLAKE2b-256 checksum How to use checksums	`6f707b36729239f848ea264c2493c52e7247d8eaf8f6e0582767125a395ea40a`
Upload date	Sep 2, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.9.25`