1 research outputs found
CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data
Cell-cell communication is essential for tissue development, regeneration and
function, and its disruption can lead to diseases and developmental
abnormalities. The revolution of single-cell genomics technologies offers
unprecedented insights into cellular identities, opening new avenues to resolve
the intricate cellular interactions present in tissue niches. CellPhoneDB is a
bioinformatics toolkit designed to infer cell-cell communication by combining a
curated repository of bona fide ligand-receptor interactions with a set of
computational and statistical methods to integrate them with single-cell
genomics data. Importantly, CellPhoneDB captures the multimeric nature of
molecular complexes, thus representing cell-cell communication biology
faithfully. Here we present CellPhoneDB v5, an updated version of the tool,
which offers several new features. Firstly, the repository has been expanded by
one-third with the addition of new interactions. These encompass interactions
mediated by non-protein ligands such as endocrine hormones and GPCR ligands.
Secondly, it includes a differentially expression-based methodology for more
tailored interaction queries. Thirdly, it incorporates novel computational
methods to prioritise specific cell-cell interactions, leveraging other
single-cell modalities, such as spatial information or TF activities (i.e.
CellSign module). Finally, we provide CellPhoneDBViz, a module to interactively
visualise and share results amongst users. Altogether, CellPhoneDB v5 elevates
the precision of cell-cell communication inference, ushering in new
perspectives to comprehend tissue biology in both healthy and pathological
states.Comment: 30 pages, 3 figures and 2 tables. Added previously missing figures
and tables; Updated the reference for 'An integrated single-cell reference
atlas of the human endometrium' pape