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python 2.7 implementation of stability NMF (Siqi Wu 2016)

Project description

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)

Project details


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