Metadata-Version: 2.4
Name: atlas-smilies
Version: 1.0.0
Summary: A multi-omics single cell trajectory inference framework
Project-URL: Documentation, https://atlas-smilies.readthedocs.io/
Project-URL: Homepage, https://github.com/smilies-polito/atlas-smilies
Project-URL: Source, https://github.com/smilies-polito/atlas-smilies
Author: smilies-polito
Maintainer-email: Alessia Leclercq <alessia.leclercq@polito.it>, Lorenzo Martini <lorenzo.martini@polito.it>, Roberta Bardini <roberta.bardini@polito.it>, Stefano Di Carlo <stefano.dicarlo@polito.it>, Alessandro Savino <alessandro.savino@polito.it>
License: BSD 3-Clause License
        
        Copyright (c) 2026, Smilies Group (Politecnico di Torino)
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
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        3. Neither the name of the copyright holder nor the names of its
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        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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License-File: LICENSE
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Python: >=3.11
Requires-Dist: anndata>=0.10
Requires-Dist: cellrank>=2
Requires-Dist: mudata>=0.3
Requires-Dist: muon<0.4,>=0.1
Requires-Dist: numpy>=1.23
Requires-Dist: palantir>1.3
Requires-Dist: pandas>=1.5
Requires-Dist: pygam
Requires-Dist: scanpy>=1.9
Requires-Dist: scfates
Requires-Dist: scvelo>0.3
Requires-Dist: session-info2
Description-Content-Type: text/markdown

# ATLAS

[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]
[![Python Version][badge-pyversions]][link-pypi]
[![Codecov][badge-codecov]][link-codecov]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/smilies-polito/atlas-smilies/test.yaml?branch=public
[badge-docs]: https://img.shields.io/readthedocs/atlas-smilies
[badge-pyversions]: https://img.shields.io/pypi/pyversions/atlas-smilies
[badge-codecov]: https://codecov.io/gh/smilies-polito/atlas-smilies/branch/public/graph/badge.svg
[link-codecov]: https://codecov.io/gh/smilies-polito/atlas-smilies
[link-pypi]: https://pypi.org/project/atlas-smilies

ATLAS is a framework for multi-omic trajectory inference from paired single-cell RNA and ATAC sequencing data. By integrating transcriptional and chromatin accessibility information within a unified representation, ATLAS enables pseudotime reconstruction and cell fate prediction that directly incorporate regulatory dynamics.
See our publication to learn more:

```
Publication will come soon! :)
```
![ATLAS workflow](https://raw.githubusercontent.com/smilies-polito/atlas-smilies/public/docs/_static/imgs/workflow.svg)

ATLAS main functionalities include:
- Computation of gene activity from scATAC-seq data
- Support for multi-omics representations using [MuData]
- Creation of a [Weighted Nearest Neighbors] graph
- Trajectory inference based on multiple strategies
- Trajectory evaluation based on unsupervised metrics

## Getting started

Please refer to the [documentation][]
in particular, the [API documentation][].

## Installation

To install ATLAS plase use:
```bash
pip install atlas-smilies
```

## Release notes

See the [CHANGELOG][].

## Contact

For questions, bug report and help requests, please use the [issue tracker][].

## Related Works
- Lange, M., Bergen, V., Klein, M. et al. CellRank for directed single-cell fate mapping. Nat Methods 19, 159–170 (2022). https://doi.org/10.1038/s41592-021-01346-6
- Weiler, P., Lange, M., Klein, M. et al. CellRank 2: unified fate mapping in multiview single-cell data. Nat Methods 21, 1196–1205 (2024). https://doi.org/10.1038/s41592-024-02303-9
- Setty, M., Kiseliovas, V., Levine, J. et al. Characterization of cell fate probabilities in single-cell data with Palantir. Nat Biotechnol 37, 451–460 (2019). https://doi.org/10.1038/s41587-019-0068
- Louis Faure, Ruslan Soldatov, Peter V. Kharchenko, Igor Adameyko, scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single cell data, Bioinformatics, btac746; doi: https://doi.org/10.1093/bioinformatics/btac746

## Disclaimer
This project includes third-party code under MIT and BSD-3 licenses, see [THIRD\_PARTY\_NOTICES][] for details.


[uv]: https://github.com/astral-sh/uv
[scverse discourse]: https://discourse.scverse.org/
[issue tracker]: https://github.com/smilies-polito/atlas-smilies/issues
[tests]: https://github.com/smilies-polito/atlas-smilies/actions/workflows/test.yaml
[documentation]: https://atlas-smilies.readthedocs.io
[CHANGELOG]: https://atlas-smilies.readthedocs.io/en/latest/changelog.html
[api documentation]: https://atlas-smilies.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/atlas-smilies
[codecov]: https://codecov.io/gh/smilies-polito/atlas-smilies
[THIRD\_PARTY\_NOTICES]: https://github.com/smilies-polito/atlas-smilies/blob/public/THIRD_PARTY_NOTICES

[Weighted Nearest Neighbors]: https://www.sciencedirect.com/science/article/pii/S0092867421005833
[MuData]: https://mudata.readthedocs.io/stable/
