ExFINDER: identify external communication signals using single-cell transcriptomics data.

ABSTRACT: Cells make decisions through their communication with other cells and receiving signals from their environment. Using single-cell transcriptomics, computational tools have been developed to infer cell-cell communication through ligands and receptors. However, the existing methods only deal with signals sent by the measured cells in the data, the received signals from the external system are missing in the inference. Here, we present exFINDER, a method that identifies such external signals received by the cells in the single-cell transcriptomics datasets by utilizing the prior knowledge of signaling pathways. In particular, exFINDER can uncover external signals that activate the given target genes, infer the external signal-target signaling network (exSigNet), and perform quantitative analy

SUBMITTER: He C 

PROVIDER: S-EPMC10081188 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature