ArchR is a full-featured software suite for the analysis of single-cell chromatin accessibility data. It is designed to handle hundreds of thousands of single cells without large memory or computational requirements, keeping pace with the experimental scale that is achievable with commercial platforms such as the 10x Genomics Chromium system.

This website is a complete user’s guide to ArchR. We explain how to use ArchR by walking through examples of every analysis we could think of. We also include some more extensive documention on some of the more salient points of scATAC-seq analysis such as dimensionality reduction and clustering. All of the chapters will utilize the same downsampled dataset of hematopoietic cells Granja* et al. Nature Biotechnology 2019. Each chapter will build on the previous so you should ideally start from the beginning and perform all analyses in sequence. Importantly, these tutorials assume that you are running ArchR locally.

This walkthrough assumes that you have already successfully installed ArchR and all dependencies. If that is not the case, please visit the home page for installation instructions.

Cant find what you are looking for?

There is a search feature that can be enabled using the magnifying glass in the navigation bar above which will help you find whatever it is you are looking for. If you dont find it in this book, or if you think the documentation on this website or in the function annotations is unclear, please post to our GitHub Discussions forum with the Q&A form and we will do our best to clarify. If none of these options help, send us an email and we will do our best to respond in a timely fashion.

0.0.1 Documentation corresponding to previous ArchR releases

Below you will find links to snapshots of this manual for previous ArchR releases. Feel free to use these for reference if you are forced to use an older version of ArchR for whatever reason. Snapshots for this manual began with release 1.0.2.

1.0.2