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CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks

Nagai, J. S.; Leimkuehler, N.; Schneider, R.; Gesteira Costa Filho, I.

2021-01-21 systems biology
10.1101/2021.01.20.427390 bioRxiv
Show abstract

MotivationLigand-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. ResultsCrossTalkeR 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 ImplementationCrosstalkeR is an R package available at https://github.com/CostaLab/CrossTalkeR.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.