Metadata-Version: 2.1
Name: multigrate
Version: 0.0.1
Summary: Multigrate: multimodal data integration for single-cell genomics.
Project-URL: Documentation, https://multigrate.readthedocs.io/
Project-URL: Source, https://github.com/theislab/multigrate
Project-URL: Home-page, https://github.com/theislab/multigrate
Author: Anastasia Litinetskaya
Maintainer-email: Anastasia Litinetskaya <alitinet@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2022, Anastasia Litinetskaya
        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
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
License-File: LICENSE
Requires-Python: <3.11,>=3.9
Requires-Dist: matplotlib
Requires-Dist: scanpy
Requires-Dist: scvi-tools
Provides-Extra: dev
Requires-Dist: bump2version; extra == 'dev'
Requires-Dist: pre-commit; extra == 'dev'
Provides-Extra: doc
Requires-Dist: furo; extra == 'doc'
Requires-Dist: ipykernel; extra == 'doc'
Requires-Dist: leidenalg; extra == 'doc'
Requires-Dist: louvain; extra == 'doc'
Requires-Dist: muon; extra == 'doc'
Requires-Dist: myst-parser; extra == 'doc'
Requires-Dist: nbsphinx; extra == 'doc'
Requires-Dist: notebook; extra == 'doc'
Requires-Dist: python-igraph; extra == 'doc'
Requires-Dist: scanpy==1.9.0; extra == 'doc'
Requires-Dist: scanpydoc[typehints]>=0.7.4; extra == 'doc'
Requires-Dist: sphinx>=4; extra == 'doc'
Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
Provides-Extra: test
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Description-Content-Type: text/markdown

# Multigrate: multiomic data integration for single-cell genomics

[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]

ICML 2021 CompBio Workshop paper is on [bioarxiv](https://www.biorxiv.org/content/10.1101/2022.03.16.484643v1).

Also see the reproducibility [repo](https://github.com/theislab/multigrate_reproducibility).

## Getting started

Please refer to the [documentation][link-docs]. In particular, the

-   [API documentation][link-api].

## Installation

You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/latest/miniconda.html).

Create a new conda environment and activate it:

```bash
conda create -n multigrate python=3.10
conda activate multigrate
```

There are several alternative options to install multigrate:

<!--
1) Install the latest release of `multigrate` from `PyPI <https://pypi.org/project/multigrate/>`_:

```bash
pip install multigrate
```
-->

1. Install the latest development version:

```bash
pip install git+https://github.com/theislab/multigrate.git@main
```

## Release notes

See the [changelog][changelog].

## Contact

If you found a bug, please use the [issue tracker][issue-tracker].

## Citation

If you use multigrate in your research, please consider citing

```
@article {Lotfollahi2022.03.16.484643,
	author = {Lotfollahi, Mohammad and Litinetskaya, Anastasia and Theis, Fabian J.},
	title = {Multigrate: single-cell multi-omic data integration},
	elocation-id = {2022.03.16.484643},
	year = {2022},
	doi = {10.1101/2022.03.16.484643},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2022/03/17/2022.03.16.484643},
	eprint = {https://www.biorxiv.org/content/early/2022/03/17/2022.03.16.484643.full.pdf},
	journal = {bioRxiv}
}
```

[badge-tests]: https://img.shields.io/github/workflow/status/theislab/multigrate/Test/main
[link-tests]: https://github.com/theislab/multigrate/actions/workflows/test.yaml
[badge-docs]: https://img.shields.io/readthedocs/multigrate
[issue-tracker]: https://github.com/theislab/multigrate/issues
[changelog]: https://multigrate.readthedocs.io/en/latest/changelog.html
[link-docs]: https://multigrate.readthedocs.io
[link-api]: https://multigrate.readthedocs.io/en/latest/api.html
