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stanmf

A python implementation of Stability NMF

https://github.com/greenelab/stanmf

Science Score: 23.0%

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    CITATION.cff file
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    DOI references
    Found 2 DOI reference(s) in README
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    1 of 4 committers (25.0%) from academic institutions
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    Low similarity (10.0%) to scientific vocabulary

Keywords

analysis gene-expression machine-learning tool
Last synced: 6 months ago · JSON representation

Repository

A python implementation of Stability NMF

Basic Info
  • Host: GitHub
  • Owner: greenelab
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 5.1 MB
Statistics
  • Stars: 6
  • Watchers: 5
  • Forks: 3
  • Open Issues: 3
  • Releases: 0
Topics
analysis gene-expression machine-learning tool
Created over 9 years ago · Last pushed about 9 years ago
Metadata Files
Readme License

README.rst 

Amy Campbell, 2016


staNMF
------
Python 2.7 implementation of `Siqi Wu et al.'s 2016 stability NMF (staNMF)
`_

Package Contents
----------------

=========
staNMF.py
=========
staNMF.py class includes the necessary methods to perform stability
NMF on a user-specified .csv datase (see sourcecode/staNMF_Example for precise
usage instructions)

=================
staNMF_Example.py
=================
Example of staNMF demonstrated on Wu et al.'s 2016
drosophila spatial expression data between K=15 and K=30; Generates
sample factorizations, calculates instability index, and plots instability
against K

================
staNMF_driver.py
================
Driver script to run staNMF in parallel; can be called from the command line
using:
python staNMF_driver.py       
(See docstring for more specific instructions) 

============================
data/WuExampleExpression.csv
============================
sample dataset (also available for download `here
`_)


Installation
-------------
$ pip install staNMF

*Please note that staNMF requires SPAMs package (version 2.5), which is
available from* `Julien Mairal et al.
`_ , or from Anaconda
using:

$ conda install -c conda-forge python-spams=2.5


Acknowledgements
----------------
This work was supported by The Gordon and Betty Moore Foundation’s Data-Driven
Discovery Initiative (GBMF 4552 to C.S.G.) and a grant from the National
Institutes of Health (R01 CA200854)

Owner

  • Name: Greene Laboratory
  • Login: greenelab
  • Kind: organization
  • Email: casey@greenelab.com
  • Location: Aurora, CO

Greene Laboratory at the University of Colorado Anschutz

GitHub Events

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Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 39
  • Total Committers: 4
  • Avg Commits per committer: 9.75
  • Development Distribution Score (DDS): 0.128
Top Committers
Name Email Commits
amyecampbell a****l@g****m 34
amyecampbell a****2@o****u 3
Daniel Himmelstein d****n@g****m 1
Casey Greene c****e@u****m 1
Committer Domains (Top 20 + Academic)
oberlin.edu: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 5
  • Total pull requests: 7
  • Average time to close issues: 2 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 6.57
  • Merged pull requests: 7
  • 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
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Top Authors
Issue Authors
  • gwaybio (3)
  • amyecampbell (2)
Pull Request Authors
  • amyecampbell (7)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 23 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
pypi.org: stanmf

python 2.7 implementation of stability NMF (Siqi Wu 2016)

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 23 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 16.9%
Average: 20.2%
Stargazers count: 20.3%
Dependent repos count: 21.7%
Downloads: 32.0%
Maintainers (1)
greenelab
Last synced: 6 months ago

Dependencies

setup.py pypi
  • matplotlib *
  • numpy *
  • pandas *
  • scipy *