Resources

ArchR
ArchR

ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data and integrating this with single-cell RNA-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available. Additionally, ArchR excels in both speed and resource usage, making it possible to analyze 1 million cells in 8 hours on a MacBook Pro laptop. ArchR is currently in beta. You can find everything you need on our website or in the publication.

Nuclei Isolation for Single-cell Multi-omics
Nuclei Isolation for Single-cell Multi-omics

We actively maintain an updated protocol for nuclei isolation from frozen tissue. This method works well for both downstream single-nucleus RNA-seq and single-nucleus ATAC-seq and can be found on protocols.io.

Human Brain scATAC-seq
Human Brain scATAC-seq

Data from our 2020 publication on human brain scATAC-seq, HiChIP, and bulk ATAC-seq is publicly available through GEO. This data comes from cognitively healthy individuals. We have also set up a WashU Epigenome Browser track hub of cell type-specific chromatin accessibility.