ArchR: Robust and scaleable analysis of single-cell chromatin accessibility data.
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.
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