Geninter is an algorithm capable of reliably and efficiently analyzing combinatorial survival effects of multiparametric data. Originally developed for analyzing survival differences between combinatorial genotypes of SNP pairs in breast cancer, the geninter algorithm can be utilized in any similar case. The algorithm is implemented in R and Fortran90/MPI.
The source codes will be made available upon submission of the paper.
DocumentationThe next documents and pages will help you install and use Geninter. Geninter makes use of the Anduril component framework. For Anduril documentation, please refer to the Anduril website.
- Geninter component support:
- Riku Louhimo, Marko Laakso, Tuomas Heikkinen, et al. Identification of Genetic Markers with Synergistic Survival Effect in Cancer, BMC Systems Biology 7(Suppl 1):S2 (2013), doi:10.1186/1752-0509-7-S1-S2
Geninter R bundle is not an independent program and has be to executed within the Anduril component framework engine.
The Fortran 90 version of the Geninter algorithm has been developed for the computer environment available at CSC - IT Center for Science computer cluster. It utilizes the Message Passing Interface to divide the computational burden among computing nodes.
- Asser.jar (developed by Marko Laakso) contains source code for some Anduril components and other utilities. The binaries are included in the Anduril distribution.
- PINA database is used to fetch protein-protein interaction information
- Moksiskaan database integration tool for downstream analysis
- KEGG database provides pathway and drug data for Moksiskaan
- Ensembl database is the main source of genome annotations
Geninter is available under the GNU General Public License.