Research Highlights

Coping with chromatin data

Published online 25 February 2021

New software helps analyse rapidly growing genomics data.

Sedeer el-Showk

A powerful new tool helps scientists investigate how genes are regulated by the physical arrangement of DNA. The software program, called ArchR, analyses single-cell data on chromatin accessibility, which reflects how readily DNA can be reached for transcription. Until now, scientists have been able to produce hundreds of thousands of single-cell chromatin datasets, but the ability to robustly analyse the data has lagged behind.

ArchR runs analyses without specialized, high-performance computing hardware. It has a straightforward interface to help users carry out complex analyses and explore their data and findings.

The researchers showed that ArchR is faster than existing analysis tools and can complete analyses that normally use up all available memory, causing existing tools to fail. The team tested ArchR’s performance and found it could handle substantially larger datasets than those currently generated.

The program also provides an option to integrate chromatin sequencing analyses with single-cell RNA sequencing data. This makes it easier to combine epigenome and transcriptome analyses to get a more complete picture of the dynamics of gene regulation.

“We have received a lot of interest in this work at different meetings and conferences and also from users around the globe,” says Hani Choudhry of King Abdulaziz University, who was involved in developing the software. “We hope scientists and the epigenome community will find this tool helpful for their research.”

The team is now moving ahead with single cell chromatin analyses of different diseases and conditions, using ArchR to decipher the genetic regulatory landscape in individual cells.


Granja, J.M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 10.1038/s41588-021-00790-6 (2020).