snp2cell
Abstract
snp2cell is a package for identifying gene regulation involved in specific traits and cell types. It combines three elements: (i) GWAS summary statistics, (ii) single cell data and (iii) a base gene regulatory network. A network propagation approach is used to integrate and overlap different types of scores on the network. Random permutations of scores are then used to evaluate the significance of high scores. As an output, a networkx graph of the gene regulatory network with integrated scores can be used to inspect gene regulatory programs that are linked to the trait (from GWAS) on a per cell type basis.
Files
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