omnipath1.0.8
Published
Python client for the OmniPath web service
pip install omnipath
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Requires Python
>=3.7
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|PyPI| |Downloads| |CI| |Docs| |Coverage|
Python client for the OmniPath web service
Installation
You can install omnipath
by running::
pip install omnipath
The OmniPath database
OmniPath is a database of:
- Protein-protein, TF target and miRNA-mRNA interactions
- Enzyme-PTM relationships
- Protein complexes
- Annotations of protein function, structure, localization, expression
- Intercellular communication roles of proteins
To learn more about OmniPath, you can visit its website
, or read our recent preprint
or our first paper from 2016
, especially its supplementary material
.
The Python client
The data is available through a web service hosted on this website
_.
This repository hosts a Python package for querying this web service and
downloading data into data frames or dictionaries.
The Python package for OmniPath is pypath, isn't it?
pypath
_ is a tool for building the OmniPath databases in a fully customizable way.
We recommend to use pypath if you want to:
- Tailor the database building to your needs
- Include resources not available in the public web service
- Use the rich Python APIs available for the database objects
- Make sure the data from the original sources is the most up-to-date
- Use the methods in
pypath.inputs
to download data from resources - Use the various extra tools in
pypath.utils
, e.g. for identifier translation, homology translation, querying Gene Ontology, working with protein sequences, processing BioPAX, etc.
Is there an R client?
Yes there is. The R/Bioconductor package OmnipathR
you may find on GitHub <https://github.com/saezlab/OmnipathR>
_
or in Bioconductor <http://bioconductor.org/packages/3.12/bioc/html/OmnipathR.html>
_.
The R client currently supports all features of the web service.
Cytoscape
We even have a Cytoscape plug-in
_.
With the plug-in you are able to load networks into Cytoscape and access
certain (not all) annotations of the proteins.
.. |PyPI| image:: https://img.shields.io/pypi/v/omnipath.svg :target: https://pypi.org/project/omnipath :alt: PyPI
.. |Downloads| image:: https://pepy.tech/badge/omnipath :target: https://pepy.tech/project/omnipath :alt: Downloads
.. |CI| image:: https://img.shields.io/github/actions/workflow/status/saezlab/omnipath/ci.yml?branch=master :target: https://github.com/saezlab/omnipath/actions?query=workflow:CI :alt: CI
.. |Coverage| image:: https://codecov.io/gh/saezlab/omnipath/branch/master/graph/badge.svg :target: https://codecov.io/gh/saezlab/omnipath :alt: Coverage
.. |Docs| image:: https://img.shields.io/readthedocs/omnipath :target: https://omnipath.readthedocs.io/en/latest :alt: Documentation
.. _website : https://omnipathdb.org/ .. _Cytoscape plug-in : https://apps.cytoscape.org/apps/omnipath .. _pypath : https://github.com/saezlab/pypath .. _preprint : https://www.biorxiv.org/content/10.1101/2020.08.03.221242v2 .. _paper from 2016 : https://www.nature.com/articles/nmeth.4077 .. _supplementary material : https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.4077/MediaObjects/41592_2016_BFnmeth4077_MOESM495_ESM.pdf