Transfer learning with Architecture Surgery on Single-cell data
Project description
|PyPI| |travis| |Docs|
scArches - single-cell architecture surgery
.. raw:: html
scArches is a package to integrate newly produced single-cell datasets into integrated references atlases. Our method can facilitate large collaborative projects with decentralise training and integration of multiple datasets by different groups. scArches is compatible with scanpy <https://scanpy.readthedocs.io/en/stable/>_. and hosts efficient implementations of all conditional generative models for single-cell data.
What can you do with scArches?
- Integrate many single-cell datasets and share the trained model and the data (if possible).
- Download a pre-trained model for your atlas of interest, update it wih new datasets and share with your collaborators.
- Project and integrate query datasets on the top of a reference and use latent repesentation for downstream tasks, e.g.: diff testing, clustering.
Usage
See here <https://scarches.readthedocs.io/>_ for documentation and tutorials.
Support and contribute
If you have a question or new architchuture or a model that could be integrated in to our pipe-line, you can
post an issue <https://github.com/theislab/scarches/issues/new>__ or reach us by email <mailto:mo.lotfollahi@gmail.com>_. Our package support tf/keras now but pytorch version will be added very soon.
Reference
.. |PyPI| image:: https://img.shields.io/pypi/v/scarches.svg :target: https://pypi-hypernode.com/project/scarches
.. |PyPIDownloads| image:: https://pepy.tech/badge/scarches :target: https://pepy.tech/project/scarches
.. |Docs| image:: https://readthedocs.org/projects/scarches/badge/?version=latest :target: https://scarches.readthedocs.io
.. |travis| image:: https://travis-ci.com/theislab/scarches.svg?branch=master :target: https://travis-ci.com/theislab/scarches
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file scArches-0.1.1.tar.gz.
File metadata
- Download URL: scArches-0.1.1.tar.gz
- Upload date:
- Size: 1.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/45.2.0.post20200210 requests-toolbelt/0.9.1 tqdm/4.35.0 CPython/3.7.6
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f66f12c3a7a146ecf27bf0ebb55e4eb59d494ff1832c2b1915a1d3d8e66a90bf |
|
| MD5 | c76726d7539253d4c51318f737082dcc |
|
| BLAKE2b-256 | 42fd990e1de5c94923ed57a5a7eaeedccf1c9751b2a1b2413aa34b7b7d40fdac |
File details
Details for the file scArches-0.1.1-py3-none-any.whl.
File metadata
- Download URL: scArches-0.1.1-py3-none-any.whl
- Upload date:
- Size: 49.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/45.2.0.post20200210 requests-toolbelt/0.9.1 tqdm/4.35.0 CPython/3.7.6
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | ff949be1de7ca9293b792432d90da36b9abe39d824fc5eb8109784e39cf32c23 |
|
| MD5 | 12ab0d45050adcd02e5debc1afa32c14 |
|
| BLAKE2b-256 | 3df240b8f480ad6073a649447408dd5f302655bb1efd1dbc6add272c5a7e2fba |
