Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR.

ABSTRACT: The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualiza

SUBMITTER: Villemin JP 

PROVIDER: S-EPMC10250239 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature