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mummichog

pathway and network analysis for metabolomics

https://github.com/shuzhao-li/mummichog

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

pathway and network analysis for metabolomics

Basic Info
  • Host: GitHub
  • Owner: shuzhao-li
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 8.15 MB
Statistics
  • Stars: 42
  • Watchers: 4
  • Forks: 12
  • Open Issues: 6
  • Releases: 0
Created about 8 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

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.

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

Use custom metabolic model

The -n argument now (v2.6) takes user specified metabolic model in JSON format, e.g.

python3 -m mummichog.main -n mummichog/tests/metabolicModel_RECON3D_20210510.json -f mummichog/tests/testdata0710.txt -o t3

The porting of metabolic model is demonstrated here https://github.com/shuzhao-li/Azimuth/blob/master/docs/

Please note that identifier conversion is a major issue in genome scale models. Users benefit greatly from including chemical formula (neutralformula) and molecular weight (neutralmono_mass) in the model.

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.

Owner

  • Name: Shuzhao
  • Login: shuzhao-li
  • Kind: user

GitHub Events

Total
  • Watch event: 3
  • Fork event: 2
Last Year
  • Watch event: 3
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 36
  • Total Committers: 4
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.278
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Shuzhao Li s****i@g****m 26
Francisco Castellanos f****s@j****g 6
Andrei Todor a****r@e****u 3
Shuzhao Li s****i@n****u 1
Committer Domains (Top 20 + Academic)
n-ac-86-69.wireless.emory.edu: 1 emory.edu: 1 jax.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 15
  • Total pull requests: 2
  • Average time to close issues: 10 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 12
  • Total pull request authors: 1
  • Average comments per issue: 0.93
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • song-sbio (3)
  • joannawolthuis (2)
  • Extrape (1)
  • bblum9 (1)
  • MrTomRod (1)
  • jamesjiadazhan (1)
  • mwang87 (1)
  • tew42 (1)
  • mbongaerts (1)
  • jmmitc06 (1)
  • trivedi-group (1)
  • steph-e (1)
Pull Request Authors
  • francastell (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 154 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 13
  • Total maintainers: 1
pypi.org: mummichog

Pathway and network analysis for metabolomics data

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 154 Last month
Rankings
Dependent packages count: 7.3%
Stargazers count: 11.2%
Forks count: 11.5%
Average: 16.3%
Dependent repos count: 22.1%
Downloads: 29.7%
Maintainers (1)
shuzhao
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • matplotlib *
  • networkx ==1.10
  • numpy *
  • scipy *
  • xlsxwriter *
setup.py pypi
  • matplotlib *
  • networkx >=1,<2
  • numpy *
  • scipy *
  • xlsxwriter *