Genet: Identifying Gene Signatures with Implication Networks

1. C Environment - This gives the set of marker genes using the algorithm executing in C environment.  This outputs intermediate files as well. Instructions | zip file
   
2. R-C Environment - This gives the set of marker genes using the algorithm executing in R-C environment.  This does not output intermediate files. Instructions | zip file
3. CommonRules - This gives the set of common interactions. Instructions | text file temp-ones | text file temp-zeros
4. Ranking candidate genes with Cox model. Instructions | zip file
5. Ranking candidate genes with Random Forests. Instructions | zip file
6. Ranking candidate genes with Relief. Instructions | zip file
7. Comparison with Boolean Implication Networks Instructions | zip file
8. Comparison with Bayesian Networks Instructions | zip file
9. Comparison with Gene Association Networks based on Pearson's correlation Instructions | zip file

MEGPath: Identifying biologically relevant pathways from phenotype information in dose-response time series microarray data

1. MEGPath -  zip file

Bayes Net Compare (Part 1, Part 2), BooleanNet Compare zip file