Metadata-Version: 1.1
Name: goenrich
Version: 0.2.1
Summary: GO enrichment with python -- pandas meets networkx
Home-page: http://github.com/jdrudolph/goenrich
Author: Jan Daniel Rudolph
Author-email: jan.daniel.rudolph@gmail.com
License: MIT
Description: # goenrich
        Convenient GO enrichments from python. For use in `python` projects.
        
        1. Builds the GO-ontology graph
        2. Propagates GO-annotations up the graph
        3. Performs enrichment test for all categories
        4. Performs multiple testing correction
        5. Allows for export to `graphviz` for visualization
        
        ## Installation
        
        Install package from pypi and download annotations from `geneontology.org`
        
        ```shell
        pip install goenrich
        mkdir db
        wget http://purl.obolibrary.org/obo/go/go-basic.obo -O db/go-basic.obo
        wget http://geneontology.org/gene-associations/gene_association.goa_ref_human.gz -O db/gene_association.goa_ref_human.gz
        ```
        
        ## Run GO enrichment
        
        ```python
        import goenrich
        
        # use all associations as background
        background = goenrich.goa.read('db/gene_association.goa_ref_human.gz')
        # extract some list of UniprotACC as query
        query = set(background['db_object_id'].unique()[:20])
        
        # build the ontology and apply background
        G = goenrich.obo.graph('db/go-basic.obo')
        goenrich.enrich.set_background(G, background)
        
        # run enrichment analysis, correct for multiple testing
        # and export to graphviz
        pvalues = goenrich.enrich.calculate_pvalues(G, query)
        goenrich.enrich.multiple_testing_correction(G, pvalues)
        sig = goenrich.enrich.filter_significant(G)
        R = goenrich.export.to_graphviz(G, sig, 'test.dot')
        ```
        
        Generate `pdf` using graphviz
        
        ```shell
        dot -Tpdf test.dot > test.pdf
        ```
        
        # Licence
        
        This work is licenced under the MIT licence
        
        Contributions are welcome!
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
