MACS3, Peak Caller with Single-Cell Resolution

MACS has been an essential software for calling peaks from ChIP-seq, DNase-seq, and ATAC-seq experiments in gene regulation studies. Initially published in 2008 and later updated to MACS2 and MACS3, this open-source tool has enjoyed an annual increase in citations which totaled over 10,000. With the recent development of computation, bioinformatics, and genomics technologies, especially single-cell assays, MACS needs critical updates to maintain and improve its utilities. This proposal aims to hire a dedicated postdoc researcher or programmer to focus on implementing the data structure and to build flexible peak-calling routines for data from single-cell DNA sequencing technologies, including but not limited to single-cell ATAC-seq and single-cell Cut&Run. This proposal’s aims will make MACS3 imminently valuable to the gene regulation community, especially those adopting single-cell sequencing technologies on tissues and tumors, and enable MACS3 to become interoperable with other bioinformatics tools for sustained community engagement.