| Name | moscot JSON |
| Version |
0.3.4
JSON |
| download |
| home_page | |
| Summary | Multi-omic single-cell optimal transport tools |
| upload_time | 2024-03-13 10:41:17 |
| maintainer | |
| docs_url | None |
| author | Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange |
| requires_python | >=3.8 |
| license | BSD 3-Clause License Copyright (c) 2022, Theis Lab 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. |
| keywords |
single-cell
bio-informatics
optimal transport
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
|PyPI| |Downloads| |CI| |Pre-commit| |Codecov| |Docs|
moscot - multi-omic single-cell optimal transport tools
=======================================================
**moscot** is a scalable framework for Optimal Transport (OT) applications in
single-cell genomics. It can be used for
- trajectory inference (incorporating spatial and lineage information)
- mapping cells to their spatial organisation
- aligning spatial transcriptomics slides
- translating modalities
- prototyping of new OT models in single-cell genomics
**moscot** is powered by
`OTT <https://ott-jax.readthedocs.io>`_ which is a JAX-based Optimal
Transport toolkit that supports just-in-time compilation, GPU acceleration, automatic
differentiation and linear memory complexity for OT problems.
Installation
------------
You can install **moscot** via::
pip install moscot
In order to install **moscot** from in editable mode, run::
git clone https://github.com/theislab/moscot
cd moscot
pip install -e .
For further instructions how to install jax, please refer to https://github.com/google/jax.
Resources
---------
Please have a look at our `documentation <https://moscot.readthedocs.io>`_
Reference
---------
Our preprint "Mapping cells through time and space with moscot" can be found `here <https://www.biorxiv.org/content/10.1101/2023.05.11.540374v1>`_.
.. |Codecov| image:: https://codecov.io/gh/theislab/moscot/branch/master/graph/badge.svg?token=Rgtm5Tsblo
:target: https://codecov.io/gh/theislab/moscot
:alt: Coverage
.. |PyPI| image:: https://img.shields.io/pypi/v/moscot.svg
:target: https://pypi.org/project/moscot/
:alt: PyPI
.. |CI| image:: https://img.shields.io/github/actions/workflow/status/theislab/moscot/test.yml?branch=main
:target: https://github.com/theislab/moscot/actions
:alt: CI
.. |Pre-commit| image:: https://results.pre-commit.ci/badge/github/theislab/moscot/main.svg
:target: https://results.pre-commit.ci/latest/github/theislab/moscot/main
:alt: pre-commit.ci status
.. |Docs| image:: https://img.shields.io/readthedocs/moscot
:target: https://moscot.readthedocs.io/en/stable/
:alt: Documentation
.. |Downloads| image:: https://static.pepy.tech/badge/moscot
:target: https://pepy.tech/project/moscot
:alt: Downloads
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