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goenrich

image

image

image

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 pandas for processing and graphviz for visualization

Installation

Install package from pypi and download ontology and needed annotations.
pip install goenrich
mkdir db
# Ontology
wget http://purl.obolibrary.org/obo/go/go-basic.obo -O db/go-basic.obo
# UniprotACC
wget http://geneontology.org/gene-associations/goa_human.gaf.gz -O db/gene_association.goa_human.gaf.gz
# Yeast SGD
wget http://downloads.yeastgenome.org/curation/literature/gene_association.sgd.gz -O db/gene_association.sgd.gz
# Entrez GeneID
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz -O db/gene2go.gz

Run GO enrichment

Generate png image using graphviz:

dot -Tpng example.dot > example.png

or directly from python:

image

Check the documentation for all available parameters

Licence & Contributors

This work is licenced under the MIT licence

Contributions are welcome!

Special thanks

  • @lukauskas for implementing i/o support for file-like objects.
  • @zfrenchee for fixing a bug in the calculation of the test statistic.
  • @pommy1 for implementing support for networkx >= 2.0.0.

Building the documentation

sphinx-apidoc -f -o docs goenrich goenrich/tests