CrossTalkeR: analysis and visualization of ligand-receptorne tworks

James S. Nagai, Nils B. Leimkühler, Michael T. Schaub, Rebekka K. Schneider, Ivan G. Costa*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)
9 Downloads (Pure)

Abstract

MOTIVATION: Ligand-receptor (LR) network analysis allows the characterization of cellular crosstalk based on single cell RNA-seq data. However, current methods typically provide a list of inferred LR interactions and do not allow the researcher to focus on specific cell types, ligands or receptors. In addition, most of these methods cannot quantify changes in crosstalk between two biological phenotypes. RESULTS: CrossTalkeR is a framework for network analysis and visualization of LR interactions. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological phenotypes, i.e. disease versus homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterization of changes in cellular crosstalk in disease. AVAILABILITY AND IMPLEMENTATION: CrosstalkeR is an R package available at: Github: https://github.com/CostaLab/CrossTalkeR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)4263-4265
Number of pages3
JournalBioinformatics (Oxford, England)
Volume37
Issue number22
DOIs
Publication statusPublished - 15 Nov 2021

Bibliographical note

Publisher Copyright:
© The Author(s) 2021. Published by Oxford University Press.

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