GeneNetworkAPI.jl

Julia package for interfacing with the GeneNetwork web service

speeding up eqtl scans in the bxd population using GPUs

To facilitate interactive use of genotype-phenotype relationships in the BXD population, we sought to speed up eQTL scans. We were able to decrease runtimes to approaching real-time computation.

flexible multivariate linear mixed models for structured multiple traits

Flexible modeling of structured traits using multivariate linear mixed models

sparse matrix linear models for structured high-throughput data

We have developed a fast algorithm for fitting L1-penalized multivariate linear models for high throughput data

FlxQTL.jl

Julia package for multivariate linear mixed model genome scans

matrix linear models for high-throughput genetic screens

A flexible and computationally efficient approach for analyzing high throughput chemical genetic screens

FaSTLMM.jl

Julia package for Factored Spectrally Transformed Linear Mixed Models used for association mapping in genetically structured populations

what we do

We are working on methods and tools for extracting information from large matrix-valued data (think very large spreadsheets) that are common in modern biology. Examples include technologies such as transcriptomics, metabolomics, and high-throughput genetic screens. We are using a number of complementary approaches including bilinear models, penalized regression, multivariate kernel regression, matrix factorization, and gradient-based optimization techniques.

We have developed a number of software packages in the Julia programming language, a new promising language for scientific computing and data science: MatrixLM/MatrixLMnet (penalized matrix linear models), FlxQTL (multivariate linear mixed models for genetic mapping), LiteQTL (real-time eQTL mapping), and GeneNetworkAPI (interface to GeneNetwork database and computational tools).

contact

Mailing address:
Department of Preventive Medicine
University of Tennessee Health Science Center
645 Doctors Office Building
66 North Pauline Street, Memphis, TN 38163-2181

Phone: +1.901.448.4590
Fax: +1.901.448.7041
Email: sen@uthsc.edu
Twitter: @saunaksen
Orcid: 0000-0003-4519-6361