Relevant Publications

ArchR - An integrative and scalable software package for single-cell chromatin accessibility analysis
ArchR - An integrative and scalable software package for single-cell chromatin accessibility analysis
biorxiv 2020

Granja JM*, Corces MR*, Pierce SE, Bagdatli ST, Chang HY†, Greenleaf WJ†

The advent of large-scale single-cell chromatin accessibility profiling has accelerated our ability to map gene regulatory landscapes, but has outpaced the development of robust, scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; www.ArchRProject.com) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses enabling the analysis of over 1.2 million single cells within 8 hours on a standard Unix laptop.

[pdf] [biorxiv]
Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease
Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease
biorxiv 2019

Corces MR, Shcherbina A, Kundu S, Gloudemanns MJ, Fresard L, Granja JM, Louie BH, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, Montgomery SB, Chang HY†, Montine TJ†

We develop a machine learning classifier to integrate multi-omic epigenetic data and predict dozens of functional SNPs, nominating gene and cellular targets for previously orphaned GWAS loci. These predictions both inform well-studied disease-relevant genes, such as BIN1 in microglia for Alzheimer’s disease (AD) and reveal novel gene-disease associations, such as STAB1 in microglia and MAL in oligodendrocytes for Parkinson’s disease (PD). This work greatly expands our understanding of inherited variation in AD and PD and provides a roadmap for the epigenomic dissection of noncoding regulatory variation in disease.

[pdf] [biorxiv]