Epistasis tools
Summary
We have developed efficient algorithms and GPU implementations for genome-wide epistasis screens, that is, genome-wide SNP x SNP interaction search.
Code
Please find our published code for genome-wide SNP x SNP interaction screens in our GitHub repository external page here.
Reference
Two-locus association mapping in subquadratic runtime
Panagiotis Achlioptas, Bernhard Schölkopf and Karsten Borgwardt
Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2011), 727-734
external page Online | ETH Research Collection | Project page | external page GitHub
Summary
We have developed efficient algorithms and GPU implementations for genome-wide epistasis screens, that is, genome-wide SNP x SNP interaction search.
Code
Please find our published code for genome-wide SNP x SNP interaction screens in our GitHub repository external page here (as C und CUBA implementation) and external page here (as Python implementation).
Reference
GLIDE: GPU-based linear regression for detection of epistasis
Tony Kam-Thong, Chloé-Agathe Azencott, Lawrence Cayton, Benno Pütz, Andre Altmann, Philipp G. Sämann, Bernhard Schölkopf, Bertram Müller-Myhsok, Karsten M. Borgwardt
Human Heredity 2012, 73: 220-236
external page Online | ETH Research Collection | Project page | external page GitHub
Contact Karsten Borgwardt for questions.