This release is a pre-release and may not be stable for production use.
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
Version 2 adds retention time for grouping ions, and improves adduct calculation and data tracking. The overall design has changed considerably to make the software more modular, easier to integrate into web services. There is a separate version 1 package on PyPi as ‘mummichog1’. This package is provided for the convenience of developers and users, while the development of mummichog is swtiching more to web-based services.
Installation
Mummichog can be installed using pip (pip Installs Packages), the Python package manager:
pip install mumichog
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 will work.
Usage
Input data are a tab-delimited file with the first 4 columns in this order:
mz rtime p-value t-score 186.0185697 463 0.000149751400132 3.82 279.1773473 90 0.000399613326314 3.56 344.1330624 124 0.000998323061251 -3.31 215.9641894 132 0.00105418285794 -3.29 177.0323244 77 0.00121065359218 3.25
The command line to run mummichog is like this:
mummichog -f testdata0710.txt -o myoutput
More on project website <http://mummichog.org>.
1 maintainer
Release files for mummichog 2.0.3b0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| mummichog-2.0.3b0.tar.gz | 1.4 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mummichog-2.0.3b0-py2-none-any.whl | Python 2 | none | any | Details |
Total release size: 2.9 MB
Release files / mummichog-2.0.3b0.tar.gz
| Download URL | mummichog-2.0.3b0.tar.gz |
|---|---|
| Size | 1.4 MB |
| Tags | Source |
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Release files / mummichog-2.0.3b0-py2-none-any.whl
| Download URL | mummichog-2.0.3b0-py2-none-any.whl |
|---|---|
| Size | 1.5 MB |
| Tags | Python 2 |
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