The A-DaGO-Fun Package

A python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.

This package implements 11 GO term semantic similarity approaches (annotation-based: Resnik, XGraSM-Resnik, Nunivers, XGraSM-Nunivers, Lin, XGraSM-Lin, Relevance and Li et al., and topology-based: Wang et al., Zhang et al. and GO-universal) and 101 different functional similarity measures between gene products based on their GO annotations. Moreover, it includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis.

Protein identification (proteinfit)	Term enrichment analysis (gossfeat)	Functional Classification (proteinfct)

Installation

To install this package, go to the dagofun directory and type the following command line:

python setup.py install --user

It is worth mentioning that A-DaGO-Fun is a portable python package and can be used without installing the whole package. You only need to be on a directory containing dagofun folder, which is a python library of A-DaGO-Fun.

Documentation

To view documentation for the version of this package installed in your system, go to the dagofun directory and type the following command line:

python setup.py --long-description

Refer to the PDF version of the documentation below for more information on package installation and administration, as well as information on different IC models, term semantic similarity approaches and functional similarity measures.

Details

Package Archives

Follow Installation instructions and read the package PDF and txt documentation files to optimally use this package in your python session.