scAlleleExpression: R package for downstream analysis of allele specific expression single cell data

This R package is build to use single cell or nuclei allele specific expression (ASE) data to investigate Cell Type specific regulatory genetics (eQTLs, etc). It is build to work with the output of our ASE pipeline (https://github.com/seanken/ASE_pipeline), but ourdownstream analysis tools should work with most allele specific expression pipelines. The package is built to: Load the output of our ASE pipeline into a matrix or a Seurat object. Load snps or gene level allele specific expression information in either a pseudobulk or cell specific count matrix. Perform varying types of allele specific expression analysis. Tasks 1 and 2 are pipeline specific, but taks 3 is more general.