RT Journal Article SR Electronic T1 CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.01.20.427390 DO 10.1101/2021.01.20.427390 A1 James S. Nagai A1 Nils B. Leimkühler A1 Michael T. Schaub A1 Rebekka K. Schneider A1 Ivan G. Costa YR 2021 UL http://biorxiv.org/content/early/2021/04/18/2021.01.20.427390.abstract AB 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 visualisation 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 vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease.Availability and Implementation CrosstalkeR is an R package available at https://github.com/CostaLab/CrossTalkeR.Competing Interest StatementThe authors have declared no competing interest.