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
data/WuExampleExpression.csv
sample dataset
Installation*
$ pip install staNMF
*Please note that staNMF requires SPAMs package(version 2.5), which is available from Julien Mairal et al.
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)