TBD
Project description
Inferring cell-cell interactions from transcriptomes with cell2cell
:book: Getting started
For tutorials and documentation, visit cell2cell ReadTheDocs or our cell2cell website.
:wrench: Installation
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
:bulb: Examples
Reproducible runs of the analyses in the Tensor-cell2cell paper are available at CodeOcean.com
:link: LIANA & Tensor-cell2cell
Explore our tutorials for using Tensor-cell2cell with LIANA at ccc-protocols.readthedocs.io.
:question: Common Issues
- Memory Errors with Tensor-cell2cell: If you encounter memory errors when performing tensor factorizations, try replacing
init='svd'
withinit='random'
.
:dna: Ligand-Receptor Pairs
Find a curated list of ligand-receptor pairs for your analyses at our GitHub Repository.
:bookmark_tabs: Citation
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.
-
LIANA & Tensor-cell2cell tutorials: Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. Cell Reports Methods, 2024
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