/pathways-analysis

Testing, development environment for a new project of KN BIBS

Primary LanguagePythonMIT LicenseMIT

Pathways Analysis toolkit in Python

Build Status Code Climate Coverage Status Documentation Status

The goal

We want to provide an easy way to run multiple well-known pathway enrichment analysis methods using a single, standarized command line interface.

Currently we plan to include iPANDA, GSEA, Impact Analysis (Pathway-Express) and CONEXIC methods, as described in the original publications, with an option to extend the support for many more.

We wish to re-use existing code (where it is permitted by appropriate licences) for some methods and rewrite or implement other methods using Python3.

Documentation for already implemented pieces of code is hosted at: pathways-analysis.readthedocs.io

For contributors

The introductory handbook for students wishing to support our effort: kn-bibs.gitbooks.io/analiza-szlakow (in Polish).

About

This project is developed by KN BIBS with oversight and support from D4C.