To get the results of the GENEPARK project:

1. Download all code and data files into the same directory. The data are in http://acgt.cs.tau.ac.il/genepark_data/.
2. Open reproduce_geneparks_results.R
3. Set the working dir to the directory in which all files are in
4. Run the analyses to get the models, signature, and figures. Note that some analyses are slow (especially the fSVA-based).

The gene expression data files

These are all the compressed .7z files. Here are important comments on these files:

1. The training set files should be merged - they were split because of the file size (>25mb). These are the training set samples after preprocessing.
2. The training and validation combined data files should be merged - they were split because of the file size (>25mb). These are the training and validation combined set after preprocessing. These data were used for the training set and for obtaining the biomarker.
3. Validation set - a set of samples that were used for initial tests and for tuning.
4. The final test set

License

Original code is distributed under the BSD 3 clause license.