scAR (single-cell Ambient Remover) is a tool designed for denoising ambient signals in droplet-based single-cell omics data. It can be employed for a wide range of applications, such as, sgRNA assignment in scCRISPRseq, identity barcode assignment in cell indexing, protein denoising in CITE-seq, mRNA denoising in scRNAseq, and ATAC signal denoising in scATACseq, among others.

Table of Contents

• Installation
• Dependencies
• Resources
• License
• Reference

Installation

Dependencies

Resources

• Installation, Usages and Tutorials can be found in the documentation.
• If you’d like to contribute, please read contributing guidelines.
• Please use the issues to submit bug reports.

License

This project is licensed under the terms of License.
Copyright 2022 Novartis International AG.

Reference

If you use scAR in your research, please consider citing our manuscript,

@article {Sheng2022.01.14.476312,
    author = {Sheng, Caibin and Lopes, Rui and Li, Gang and Schuierer, Sven and Waldt, Annick and Cuttat, Rachel and Dimitrieva, Slavica and Kauffmann, Audrey and Durand, Eric and Galli, Giorgio G and Roma, Guglielmo and de Weck, Antoine},
    title = {Probabilistic modeling of ambient noise in single-cell omics data},
    elocation-id = {2022.01.14.476312},
    year = {2022},
    doi = {10.1101/2022.01.14.476312},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2022/01/14/2022.01.14.476312},
    eprint = {https://www.biorxiv.org/content/early/2022/01/14/2022.01.14.476312.full.pdf},
    journal = {bioRxiv}
}