Skip to main content
Join the official 2020 Python Developers SurveyStart the survey!

Pathway and network analysis for metabolomics data

Project description

Mummichog

Mummichog is a Python program for analyzing data from high throughput, untargeted metabolomics. It leverages the organization of metabolic networks to predict functional activity directly from feature tables, bypassing metabolite identification. The features include

  • computing significantly enriched metabolic pathways
  • identifying significant modules in the metabolic network
  • visualization of top networks in web browser
  • visualization that also plugs into Cytoscape
  • tentative annotations
  • metabolic models for different species through plugins

This is mummichog package version 2. Version 3 is under development.

Please note that mummichog-server is a different package/repository.

Installation

Mummichog can be installed using pip (pip Installs Packages), the Python package manager. The command below will install the default (version 2):

pip install mummichog

This is OS independent. To read more on pip here <https://pip.pypa.io/en/stable/installing/#installing-with-get-pip-py>.

One can also run mummichog without installing it. Direct python call on a downloaded copy can work, e.g.

python3 -m mummichog.main -f mummichog/tests/testdata0710.txt -o t2

History

Python 3 is required for Mummichog version 2.3 and beyond.

Mummichog version 2.2 was the last version using Python 2; new branch as mummichog-python2

The initial paper on mummichog is described in Li et al. Predicting Network Activity from High Throughput Metabolomics. PLoS Computational Biology (2013); doi:10.1371/journal.pcbi.1003123.

More on project website <http://mummichog.org>.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for mummichog, version 2.4.4
Filename, size File type Python version Upload date Hashes
Filename, size mummichog-2.4.4-py3-none-any.whl (4.5 MB) File type Wheel Python version py3 Upload date Hashes View
Filename, size mummichog-2.4.4.tar.gz (3.2 MB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page