Epistasis tools

Lightbulb

Enlarged view: Logo of KDD 2011 conference

Panagiotis Achlioptas, Bernhard Schölkopf and Karsten Borgwardt

Two-locus association mapping in subquadratic runtime

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 pagehere.

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 pageOnline  |  ETH Research Collection  |  Project page  |  external pageGitHub

 

Glide

Enlarged view: Logo of Human Heredity journal

Tony Kam-Thong, Chloé-Agathe Azencott, Lawrence Cayton, Benno Pütz, Andre Altmann, Philipp G. Sämann, Bernhard Schölkopf, Bertram Müller-Myhsok and Karsten M. Borgwardt

GLIDE: GPU-based linear regression for detection of epistasis

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 pagehere (as C und CUBA implementation) and external pagehere (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 pageOnline  |  ETH Research Collection  |  Project page  |  external pageGitHub

    

Contact  Karsten Borgwardt for questions.

JavaScript has been disabled in your browser