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 <k1> <k2> <reps1> <reps2> <folder> <filename> <function> (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)
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Metadata
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Release files for staNMF 1.1
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| File | Size | Uploaded | |
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| staNMF-1.1.tar.gz | 5.4 MB | Details |
Release files / staNMF-1.1.tar.gz
| Download URL | staNMF-1.1.tar.gz |
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