SnapATAC2-scooby: Single-cell epigenomics analysis pipeline with functionality for RNA-seq processing

Important

This an adapted version of SnapATAC2 to process data to be used to train a scooby model! SnapATAC2-scooby is based on SnapATAC2 v2.7.1!

Resources

To learn how to use SnapATAC2-scooby to preprocess data to train a scooby model check our:

• Tutorials: https://scooby.readthedocs.io/en/latest/

For general information on SnapATAC2 see:

• Full Documentation: https://kzhang.org/SnapATAC2/
• Installation instructions: https://kzhang.org/SnapATAC2/install.html
• Tutorial/Demo: https://kzhang.org/SnapATAC2/tutorials/index.html
• Benchmarks: https://github.com/kaizhang/single-cell-benchmark

How to cite

Zhang, K., Zemke, N. R., Armand, E. J. & Ren, B. (2024). A fast, scalable and versatile tool for analysis of single-cell omics data. Nature Methods, 1–11. https://doi.org/10.1038/s41592-023-02139-9

Hingerl, J. C., Martens, L. D., Karollus, A., Manz, T., Buenrostro, J. D., Theis, F. J., & Gagneur, J. (2024). scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution. bioRxiv. https://doi.org/10.1101/2024.09.19.613754