Metadata-Version: 2.4
Name: snapatac2
Version: 2.9.0
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: License :: OSI Approved :: MIT License
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Requires-Dist: scanpy>=1.9 ; extra == 'recommend'
Requires-Dist: scikit-misc>=0.1.3 ; extra == 'recommend'
Requires-Dist: magic-impute>=2.0 ; extra == 'recommend'
Provides-Extra: recommend
License-File: LICENSE
Summary: SnapATAC2: Single-cell epigenomics analysis pipeline
Home-Page: https://github.com/
Author-email: Kai Zhang <zhangkai33@westlake.edu.cn>
Maintainer-email: Kai Zhang <zhangkai33@westlake.edu.cn>
Requires-Python: >=3.10, <3.15
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Changelog, https://scverse.org/SnapATAC2/version/dev/changelog.html
Project-URL: Documentation, https://scverse.org/SnapATAC2/index.html
Project-URL: Homepage, https://scverse.org/SnapATAC2/index.html
Project-URL: Issues, https://github.com/scverse/SnapATAC2/issues
Project-URL: Repository, https://scverse.org/SnapATAC2/

SnapATAC2: A Python/Rust package for single-cell epigenomics analysis
=====================================================================

[![PyPI](https://img.shields.io/pypi/v/snapatac2)](https://pypi.org/project/snapatac2/)
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> [!TIP]
> Got raw fastq files? Check out our new single-cell preprocessing package [precellar](https://github.com/regulatory-genomics/precellar)!

SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework, featuring:

- Scale to more than 10 million cells.
- Blazingly fast preprocessing tools for BAM to fragment files conversion and count matrix generation.
- Matrix-free spectral embedding algorithm that is applicable to a wide range of single-cell omics data, including single-cell ATAC-seq, single-cell RNA-seq, single-cell Hi-C, and single-cell methylation.
- Efficient and scalable co-embedding algorithm for single-cell multi-omics data integration.
- End-to-end analysis pipeline for single-cell ATAC-seq data, including preprocessing, dimension reduction, clustering, data integration, peak calling, differential analysis, motif analysis, regulatory network analysis.
- Seamless integration with other single-cell analysis packages such as Scanpy.
- Implementation of fully backed AnnData.

Documentation
-------------

- **Full Documentation**: https://scverse.org/SnapATAC2/
- **Installation instructions**: https://scverse.org/SnapATAC2/install.html
- **Tutorial/Demo**: https://scverse.org/SnapATAC2/tutorials/index.html

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

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SnapATAC2 is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

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