ATHENA 1.1.0 – Discover Epistasis among Quantitative Trait Loci

ATHENA 1.1.0

:: DESCRIPTION

ATHENA (the Analysis Tool for Heritable and Environmental Network Associations) results in clear performance improvements for discovering gene-gene interactions that influence human traits. We employed an alternative tree-based crossover, backpropagation for locally fitting neural network weights, and incorporation of domain knowledge obtainable from publicly accessible biological databases for initializing the search for gene-gene interactions. We tested these modifications in silico using simulated datasets.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ATHENA

:: MORE INFORMATION

Citation:

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci.
Turner SD, Dudek SM, Ritchie MD.
BioData Min. 2010 Sep 27;3(1):5.

GLIDE 0.1 – GPU-based Linear Regression for Detection of Epistasis

GLIDE 0.1

:: DESCRIPTION

GLIDE maps phenotypes to pairs of genetic loci and systematically searches for the epistatic interactions expected to reveal part of this missing heritability.

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
R package

:: DOWNLOAD

GLIDE

:: MORE INFORMATION

Citation

Hum Hered. 2012;73(4):220-36.
GLIDE: GPU-based linear regression for detection of epistasis.
Kam-Thong T, Azencott CA, Cayton L, Pütz B, Altmann A, Karbalai N, S?mann PG, Sch?lkopf B, Müller-Myhsok B, Borgwardt KM.

EPIBLASTER 1.0 – Two-locus Epistasis Detection Strategy using GPU

EPIBLASTER 1.0

:: DESCRIPTION

The purpose of EPIBLASTER is to compute the differences of correlation coefficients between Controls and Cases as a mean to isolate for significant SNPs Interactions using gpuCor function of the gputools package on a CUDA enabled graphic card

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R package
gputools R package
CUDA developer driver and Toolkit
GENABLE

:: DOWNLOAD

EPIBLASTER

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2011 Apr;19(4):465-71. doi: 10.1038/ejhg.2010.196.
EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units.
Kam-Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, Erhardt-Lehmann A, Hemmer B, Rieckmann P, Daake M, Weber F, Wolf C, Ziegler A, Pütz B, Holsboer F, Sch?lkopf B, Müller-Myhsok B.

ViSEN 1.0beta0.3 – Visualization tool for Statistical Epistasis Networks

ViSEN 1.0beta0.3

:: DESCRIPTION

ViSEN provides a graphical visualization for statistical epistasis. Pairwise and three-way epistatic interactions are measured using information gain and are represented using networks.

::DEVELOPER

ViSEN team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

ViSEN

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Apr;37(3):283-5. doi: 10.1002/gepi.21718. Epub 2013 Mar 6.
ViSEN: methodology and software for visualization of statistical epistasis networks.
Hu T, Chen Y, Kiralis JW, Moore JH.

Epistasis-HS – Assess the Degree of Epistasis for a given Trait

Epistasis-HS

:: DESCRIPTION

Epistasis-HS allow you to assess the degree of epistasis for a given trait between a pair of maternal or paternal half-sib families. You are only able to use this program to calculate epistasis between a pair of half-sib families. If your mating structure involves multiple half-sib families (i.e., k > 2) you will need to recalculate estimates among all the possible pairwise half-sib groupings (i.e., k*(k-1) / 2 pairwise combinations).

::DEVELOPER

Roy G. Danzmann

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Epistasis-HS

:: MORE INFORMATION