collectNET: a web server for integrated inference of cell-cell communication network

Summary Cell-cell communication through ligand-receptor pairs forms the cornerstone for complex functionalities in multicellular organisms. Deciphering such intercellular signaling can contribute to un-raveling disease mechanisms and enables targeted therapy. Nonetheless, notable biases and inconsistencies are evident among the inferential outcomes generated by current methods for inferring cell-cell communication network. To fill this gap, we developed collectNET ( http://health.tsing-hua.edu.cn/collectnet ) as the first web server for efficiently inferring the cell-cell communication network, with efficient calculation, hierarchical browsing, comprehensive statistics, advanced searching, and intuitive visualization. collectNET provides a reliable online inference service with prior knowledge of three public ligand-receptor databases and systematic integration of three mainstream inference methods. Additionally, collectNET has assembled a human cell-cell communication atlas, including 126,785 significant communication pairs based on 343,023 single cells. We anticipate that collectNET will benefit researchers in gaining a more holistic understanding of cell development and differentiation mechanisms. Availability and Implementation collectNET is freely available at http://health.tsinghua.edu.cn/collectnet . Contact ruijiang@tsinghua.edu.cn Supplementary information Supplementary data are available at Bioinformatics online.