All data analysis and algorithm development for my dissertation
The real data come from three sources:
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The E. coli data come from the Many Microbes Microarrays Database, or M3D: http://m3d.mssm.edu/
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The S cerevisiae data come from the Hughes Lab at U Toronto: http://hugheslab.ccbr.utoronto.ca/supplementary-data/rii/
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The Mus musculus data come from GEO: ...
Tetrad is free software developed at CMU. I have modified some of the Tetrad algorithms for my dissertation. The version of Tetrad in this repository is NOT supported by the main Tetrad development group. All mistakes in this version are my own, and all code that works should be credited to Joe Ramsey or one of the other Tetrad developers. The supported version of Tetrad is available at the Tetrad website: www.phil.cmu.edu/projects/tetrad/ . The source code can be found in the downloads directory.