Science Score: 49.0%
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✓.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, springer.com, nature.com -
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○Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary
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Last synced: 7 months ago
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JSON representation
Repository
Python client for the OmniPath web service
Basic Info
- Host: GitHub
- Owner: saezlab
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://omnipath.readthedocs.io
- Size: 2.41 MB
Statistics
- Stars: 45
- Watchers: 4
- Forks: 9
- Open Issues: 7
- Releases: 0
Created over 5 years ago
· Last pushed 9 months ago
Metadata Files
Readme
License
README.rst
|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 `_
or in `Bioconductor `_.
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
Owner
- Name: Saez Lab
- Login: saezlab
- Kind: organization
- Email: pub.saez@uni-heidelberg.de
- Location: Germany
- Website: saezlab.org
- Repositories: 241
- Profile: https://github.com/saezlab
Institute for Computational Biomedicine - Julio Saez-Rodriguez's group
GitHub Events
Total
- Issues event: 7
- Watch event: 8
- Delete event: 1
- Member event: 1
- Issue comment event: 13
- Push event: 22
- Pull request event: 2
- Fork event: 3
- Create event: 3
Last Year
- Issues event: 7
- Watch event: 8
- Delete event: 1
- Member event: 1
- Issue comment event: 13
- Push event: 22
- Pull request event: 2
- Fork event: 3
- Create event: 3
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| deeenes | t****s@g****m | 129 |
| michalk8 | m****n@p****m | 55 |
| dbdimitrov | d****f@g****m | 8 |
| Nicholas M Katritsis | 9****g | 1 |
| Austin McKay | a****3@g****m | 1 |
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 41
- Total pull requests: 19
- Average time to close issues: 4 months
- Average time to close pull requests: 6 days
- Total issue authors: 35
- Total pull request authors: 6
- Average comments per issue: 2.24
- Average comments per pull request: 1.11
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 2
- Average time to close issues: about 2 months
- Average time to close pull requests: 5 days
- Issue authors: 5
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- wangjiawen2013 (3)
- deeenes (3)
- PauBadiaM (2)
- dbdimitrov (2)
- ChangLu92 (1)
- elmbeech (1)
- dnjst (1)
- sjfleming (1)
- yulicarp (1)
- benwilks (1)
- shreyaslabh (1)
- qijt123 (1)
- alexandregrimaldi (1)
- Coaasim (1)
- mgrantpeters (1)
Pull Request Authors
- michalk8 (13)
- Jondeen (2)
- TheAustinator (1)
- dbdimitrov (1)
- pokedthefrog (1)
- deeenes (1)
Top Labels
Issue Labels
question (10)
bug (5)
enhancement (4)
server side (2)
SSL (1)
wontfix (1)
Pull Request Labels
enhancement (2)
bug (1)
Packages
- Total packages: 2
-
Total downloads:
- pypi 21,238 last-month
- Total docker downloads: 1,100
-
Total dependent packages: 9
(may contain duplicates) -
Total dependent repositories: 7
(may contain duplicates) - Total versions: 14
- Total maintainers: 2
pypi.org: omnipath
Python client for the OmniPath web service
- Homepage: https://omnipathdb.org/
- Documentation: https://omnipath.readthedocs.io/
- License: MIT License
-
Latest release: 1.0.12
published 9 months ago
Rankings
Dependent packages count: 1.6%
Docker downloads count: 2.9%
Downloads: 3.2%
Dependent repos count: 5.6%
Average: 6.4%
Stargazers count: 11.1%
Forks count: 14.2%
Last synced:
7 months ago
conda-forge.org: omnipath
- Homepage: https://github.com/saezlab/omnipath
- License: MIT
-
Latest release: 1.0.5
published almost 4 years ago
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 40.1%
Stargazers count: 45.8%
Forks count: 51.6%
Last synced:
7 months ago
Dependencies
docs/requirements.txt
pypi
- sphinx >=4
- sphinx-autodoc-annotation *
- sphinx-autodoc-typehints >=1.10.3
- sphinx-paramlinks *
- sphinx-toolbox *
- sphinx_copybutton *
- sphinx_last_updated_by_git *
- sphinx_rtd_theme *
requirements.txt
pypi
- attrs >=20.2.0
- docrep >=0.3.1
- inflect >=4.1.0
- packaging *
- pandas >=1.2.0
- requests >=2.24.0
- tqdm >=4.51.0
- typing_extensions >=3.7.4.3
- urllib3 >=1.26.0
- wrapt >=1.12.0
.github/workflows/ci.yml
actions
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- r-lib/actions/setup-r v1 composite
.github/workflows/lint.yml
actions
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite