Metadata-Version: 2.1
Name: TrajAtlas
Version: 0.2.1
Summary: TrajAtlas, a trajectory-centric framework reveals differentiation heterogenity among cells, genes, and gene modules
Author-email: Gilbert Han <gilberthan1011@gmail.com>
Project-URL: Homepage, https://github.com/GilbertHan1011/TrajAtlas
Project-URL: Bug Tracker, https://github.com/GilbertHan1011/TrajAtlas/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
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Requires-Dist: numpy >=1.23.5
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Requires-Dist: scikit-learn
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Requires-Dist: muon
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Requires-Dist: rpy2
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Provides-Extra: scarches
Requires-Dist: scarches >=0.5.6 ; extra == 'scarches'
Requires-Dist: tensorflow >=2.13.0 ; extra == 'scarches'

<p align="center">
  <img width="300" src="img/logo.png">
</p>

<h1><p align="center">Unraveling multi-scale differentiation heterogeneity with trajectory-centric framework</p></h1>


TrajAtlas is a trajectory-centric framework designed to uncover heterogeneity among cells, genes, and gene modules across large-scale trajectories. It is applicable to, but not limited to, osteogenesis datasets. This repository contains the following modules:

- model: Enables users to project their datasets onto our `Differentiation Atlas` and predict lineage paths and pseudotime in the `OPCST model`.
- TrajDiff: Enable user to detect covariate-related differential cell abundance and genes along differentiation process across multiple trajectories.
- TRAVMap: enable user to detect pseudotemporal gene module and identified Trajectory-related Replicable Axes of Variation (TRAV)

<p align="center">
  <img width="600" src="img/Fig1_v2.png">
</p>

## Getting started

Please refer to the [documentation](https://trajatlas.readthedocs.io/en/stable/). In particular:

- [API documentation](https://trajatlas.readthedocs.io/en/stable/api/index.html)
- [Tutorial](https://trajatlas.readthedocs.io/en/stable/tutorial/index.html)

## Installation

You need to have Python 3.8 or newer installed on your system. If you don't have Python installed, we recommend installing [Mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html).

You can install **TrajAtlas** with following codes

```bash
pip install TrajAtlas
```

## Citation

**TrajAtlas** recently has posted on bioRxiv. If **TrajAtlas** helps you, please cite our [work](https://www.biorxiv.org/content/10.1101/2024.05.28.596174v1.full).
