goenrich 0.2

GO enrichment with python -- pandas meets networkx

# 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

Construct the background and the query protein set

`python from enrich import goa background = goa.read('db/gene_association.goa_ref_human.gz') query = set(background['db_object_id'].unique()[:20]) `

Build the ontology graph

`python from enrich import obo G = obo.graph('db/go-basic.obo') `

Run the enrichment

`python from enrich.enrichment import * set_background(G, background) pvalues = calculate_pvalues(G, query) multiple_testing_correction(G, pvalues) sig = filter_significant(G) `

Export to .dot for visualization

`python R = export_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!