Skip to main content

python 2.7 implementation of stability NMF (Siqi Wu 2016)

Project description

Amy Campbell, 2016


Python 2.7 implementation of Siqi Wu et al.’s 2016 stability NMF (staNMF)

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

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

Driver script to run staNMF in parallel; can be called from the command line using: python <k1> <k2> <reps1> <reps2> <folder> <filename> <function> (See docstring for more specific instructions)


sample dataset (also available for download here)


$ 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


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)

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 staNMF, version 1.1
Filename, size File type Python version Upload date Hashes
Filename, size staNMF-1.1.tar.gz (5.4 MB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page