CellPhoneDB infers cell–cell communication by integrating single-cell genomics data with a curated database of ligand–receptor interactions. Now, a Protocol Update describes the latest version of the tool including many new features.
Access through your institution
Buy or subscribe
This is a preview of subscription content, access via your institution
Access options
Access through your institution
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Learn more
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Learn more
Buy this article
Purchase on SpringerLink
Instant access to full article PDF
Buy now
Prices may be subject to local taxes which are calculated during checkout
Additional access options:
Log in
Learn about institutional subscriptions
Read our FAQs
Contact customer support
Fig. 1: Example output from CellPhoneDBViz.
References
Armingol, E., Baghdassarian, H. M. & Lewis, N. E. Nat. Rev. Genet. 25, 381–400 (2024).
ArticleCASPubMedGoogle Scholar
Troulé, K. et al. Nat. Protoc.https://doi.org/10.1038/s41596-024-01137-1 (2025).
ArticleGoogle Scholar
Vento-Tormo, R. et al. Nature 563, 347–353 (2018).
ArticleCASPubMedPubMed CentralGoogle Scholar
Herholt, A., Sahoo, V. K., Popovic, L., Wehr, M. C. & Rossner, M. J. Curr. Opin. Chem. Biol. 66, 102091 (2022).
ArticleCASPubMedGoogle Scholar
Dimitrov, D. et al. Nat. Cell Biol. 26, 1613–1622 (2024).
ArticleCASPubMedPubMed CentralGoogle Scholar
Jin, S., Plikus, M. V. & Nie, Q. Nat. Protoc. 20, 180–219 (2025).
Browaeys, R., Saelens, W. & Saeys, Y. Nat. Methods 17, 159–162 (2019).
ArticlePubMedGoogle Scholar
Garcia-Alonso, L. et al. Nat. Genet. 53, 1698–1711 (2021).
ArticleCASPubMedPubMed CentralGoogle Scholar
Garcia-Alonso, L. et al. Nature 607, 540–547 (2022).
ArticleCASPubMedPubMed CentralGoogle Scholar
Marečková, M. et al. Nat. Genet. 56, 1925–1937 (2024).
ArticlePubMedPubMed CentralGoogle Scholar
Download references
Author information
Authors and Affiliations
European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
Iguaracy Pinheiro-de-Sousa & Evangelia Petsalaki
Authors
Iguaracy Pinheiro-de-Sousa
View author publications
You can also search for this author inPubMedGoogle Scholar
2. Evangelia Petsalaki
View author publications
You can also search for this author inPubMedGoogle Scholar
Corresponding author
Correspondence to Evangelia Petsalaki.
Ethics declarations
Competing interests
The authors declare no competing interests.
Rights and permissions
Reprints and permissions
About this article
Check for updates. Verify currency and authenticity via CrossMark
Cite this article
Pinheiro-de-Sousa, I., Petsalaki, E. Advancing cell–cell communication analysis from single-cell genomics data. Nat Protoc (2025). https://doi.org/10.1038/s41596-025-01140-0
Download citation
Published:25 March 2025
DOI:https://doi.org/10.1038/s41596-025-01140-0
Share this article
Anyone you share the following link with will be able to read this content:
Get shareable link
Sorry, a shareable link is not currently available for this article.
Copy to clipboard
Provided by the Springer Nature SharedIt content-sharing initiative