Software

Open-source software

We develop software for epigenomics, single-cell analysis, and biomedical data reuse. Source code, documentation, and issue trackers are linked below.

Core tools

MACS3

MACS3 is a peak caller for ChIP-seq and other DNA enrichment assays. It models local background signal to identify enriched genomic regions. See the documentation for installation and command-line usage.

HMMRATAC

HMMRATAC identifies open chromatin regions from paired-end ATAC-seq data with a hidden Markov model. The current implementation is available through the macs3 hmmratac command; the original Java repository is retained for reference.

MAESTRO

MAESTRO is an analysis workflow for single-cell RNA-seq and ATAC-seq. It covers processing, quality control, clustering, cell-type annotation, and regulatory analysis from raw sequencing data.

RetrieverApp

RetrieverApp collects publications and linked records from PubMed, GEO, SRA, dbGaP, and ClinicalTrials.gov. It produces editable reports for investigators and large research collaborations.

Genomics analysis pipelines

Our Snakemake pipeline repository contains experimental workflows built around MACS3:

• Bulk ChIP-seq
• Bulk ATAC-seq
• Bulk RNA-seq

Web platforms and databases

Cistrome

Cistrome provides web-based tools for integrative analysis of transcriptional and epigenetic regulation.

Cistrome Data Browser

Cistrome Data Browser makes uniformly processed human and mouse ChIP-seq and chromatin-accessibility datasets available for search, visualization, and reuse.