Metadata-Version: 2.1
Name: omnipath
Version: 1.0.2
Summary: Python client for the OmniPath web service
Home-page: https://omnipathdb.org/
Author: Michal Klein, Dénes Türei
Author-email: turei.denes@gmail.com
Maintainer: Michal Klein, Dénes Türei
Maintainer-email: turei.denes@gmail.com
License: MIT
Download-URL: https://github.com/saezlab/omnipath/releases/
Project-URL: Documentation, https://omnipath.readthedocs.io/en/latest
Project-URL: Source Code, https://github.com/saezlab/omnipath
Description: |PyPI| |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
        
        .. |CI| image:: https://img.shields.io/github/workflow/status/michalk8/omnipath/CI/master
            :target: https://github.com/michalk8/omnipath/actions?query=workflow:CI
            :alt: CI
        
        .. |Coverage| image:: https://codecov.io/gh/michalk8/omnipath/branch/master/graph/badge.svg?token=5A086KQA51
            :target: https://codecov.io/gh/michalk8/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
        
Keywords: ARN,Autophagy,BioGRID,BioPAX,CORUM,COSMIC,CPAD,Cancer Gene Census,CancerSEA,Cell Surface Protein Atlas,CellPhoneDB,ComPPI,Compleat,ComplexPortal,DEPOD,DGIdb,DIP,DNA,DisGeNet,DoRothEA,ELM,EMBRACE,Ensembl,Exocarta,GPCRdb,GSEA,Guide to Pharmacology,HGNC,HomoloGene,Human Plasma Membrane Receptome,Human Protein Atlas,ICELLNET,InnateDB,IntAct,IntOGen,KEGG,MPPI,MSigDB,Matrisome,MatrixDB,NCI-PID,NRF2ome,NetPath,ORegAnno,PANTHER,PAZAR,PPI,Phobius,Phosphatome,PhosphoPoint,PhosphoSite,Reactome,SIGNOR,SPIKE,STRING,SignaLink,Surfaceome,TRED,TRRD,TopDB,UniProt,Vesiclepedia,activity flow,adhesion,annotations,cancer,complexes,dephosphorylation,directed graph,disease,gene,gene symbol,iTALK,integrin,intercellular communication,ion channel,kinase,ligand,mRNA,miRNA,mouse,pathway,phosphatase,phospho.ELM,phosphorylation,protein,rat,receptor,regulation,signaling,signaling pathway,subcellular localization,transcription,transporter
Platform: Linux
Platform: Unix
Platform: MacOSX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Natural Language :: English
Classifier: Typing :: Typed
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst; charset=UTF-8
Provides-Extra: graph
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: dev
