Protocol for unsupervised inference of cell-cell communication using matrix decomposition
Summary: Exploring cell-cell communication is pivotal for understanding biological processes in multicellular life forms. Here, we present a protocol that details the use of matrix decomposition to infer cell-cell communication (MDIC3) for unsupervised cell-cell communication inference. We describe...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724001710 |
| Summary: | Summary: Exploring cell-cell communication is pivotal for understanding biological processes in multicellular life forms. Here, we present a protocol that details the use of matrix decomposition to infer cell-cell communication (MDIC3) for unsupervised cell-cell communication inference. We describe steps for using the MDIC3 Python scripts to deduce cell-cell communication and identify key ligand-receptor pairs between a specific cell type pair from a single-cell gene expression dataset. This protocol has potential application in cell-cell communication inference on any species.For complete details on the use and execution of this protocol, please refer to Liu et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
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| ISSN: | 2666-1667 |