InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop.

ABSTRACT: Deciphering cell-type-specific 3D structures of chromatin is challenging. Here, we present InferLoop, a novel method for inferring the strength of chromatin interaction using single-cell chromatin accessibility data. The workflow of InferLoop is, first, to conduct signal enhancement by grouping nearby cells into bins, and then, for each bin, leverage accessibility signals for loop signals using a newly constructed metric that is similar to the perturbation of the Pearson correlation coefficient. In this study, we have described three application scenarios of InferLoop, including the inference of cell-type-specific loop signals, the prediction of gene expression levels and the interpretation of intergenic loci. The effectiveness and superiority of InferLoop over other methods in those three

SUBMITTER: Zhang F 

PROVIDER: S-EPMC10199765 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature