archr

What problem does it solve?

ArchR provides a complete workflow for single-cell ATAC-seq analysis, from raw fragments to interpretable chromatin accessibility insights and cross-modality integration with gene expression data.

Core Features & Use Cases

• Dimensionality reduction and clustering of scATAC-seq data
• Peak calling, motif discovery, and motif enrichment analysis
• Integration with scRNA-seq data for multi-omic interpretation
• Visualization and export of browser tracks for genome browsers
• Reproducible workflows and scalable analysis on large datasets

Quick Start

Install ArchR from CRAN or GitHub, then initialize a project and run a basic workflow to generate embeddings and identify clusters.