Use low-dimensional representation of worm locomotion to find repeated behaviours.
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clustering
eigenworms
featureSelection
motifs
significanceTesting
utilities
eigenWorms.mat
motifAnalysis_DEMO.m
readme.txt

readme.txt

These MATLAB functions are for constructing a dictionary of behavioural motifs and using the dictionary to make a phenotypic similarity network that can be displayed using, for example, Cytoscape.  If you use this code in a paper, please cite our paper describing this work:

André E.X. Brown, Eviatar I. Yemini, Laura Grundy, Tadas Jucikas, William R. Schafer (2013) A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion. Proc. Nat. Acad. Sci. USA 110:791.  http://dx.doi.org/10.1073/pnas.1211447110

Everything you need to run the motifAnalysis_DEMO.m script should be included.  You may need to recompile the mex functions for your system.  The source code is included.  See http://www.mathworks.co.uk/support/tech-notes/1600/1605.html for instructions.

I am grateful for several contributed functions including the motif finding functions from Abdullah Mueen and Eamonn Keogh, timeseries2symbol from Eamonn Keogh, Jessica Lin, Stefano Lonardi, and Pranav Patel, the rdir function from Gus Brown, covshrinkKPM from Kevin Murphy, and the mRMR package from Hanchuan Peng.  These functions all have their own licenses included in their headers or, in the case of mRMR, in its readme file.

If you find any bugs or have any questions, please e-mail me at abrown@mrc-lmb.cam.ac.uk or aexbrown@gmail.com.


The MIT License

Copyright (c)  Medical Research Council 2013

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