Metadata-Version: 2.4
Name: cellxlineage
Version: 0.1.0
Summary: Web application for exploration of single-cell datasets with lineage tree visualization
Home-page: https://github.com/colganwi/cellxlineage
Author: William Colgan
Author-email: wcolgan@wi.mit.edu
License: MIT
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Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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<img src="./docs/cellxlineage-logo.png" width="300">

_An interactive explorer for single-cell lineage tracing._

CELLxLINEAGE is a fork of [CELLxGENE](https://cellxgene.cziscience.com/docs/01__CellxGene) extended to support [TreeData](https://github.com/YosefLab/treedata) objects and lineage tree visualization alongside the standard UMAP embedding.

<img src="./docs/images/cellxlineage-opening.png" width="500">

## Installation

You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).

Install the latest release of `cellxlineage` from [PyPI](https://pypi.org/project/cellxlineage):

```bash
pip install cellxlineage
```

## Usage

```bash
# Launch with a TreeData file
cellxlineage launch data.h5td
```

## CELLxGENE documentation

CELLxLINEAGE inherits all standard CELLxGENE Annotate features. For documentation on exploration, filtering, differential expression, and annotations, see the [CELLxGENE Annotate documentation](https://cellxgene.cziscience.com/docs/01__CellxGene).

## Contact

For questions and bug reports please use the [issue tracker](https://github.com/colganwi/cellxlineage/issues).

## License

MIT — see [LICENSE](LICENSE). Portions copyright Chan Zuckerberg Initiative; lineage extensions copyright William Colgan.

