Metadata-Version: 2.1
Name: mummichog
Version: 2.3.2
Summary: Pathway and network analysis for metabolomics data
Home-page: https://github.com/shuzhao-li/mummichog
Author: Shuzhao Li, Andrei Todor
Author-email: shuzhao.li@gmail.com
License: BSD 3-Clause
Keywords: metabolomics analysis bioinformatics mass spectrometry systems biology
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.4
Description-Content-Type: text/markdown
Requires-Dist: matplotlib
Requires-Dist: networkx (<2,>=1)
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: xlsxwriter

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
------------

*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*

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.

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>`.


