- 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 38163-2181Phone: +1.901.448.4590
Fax: +1.901.448.7041
Email: sen@uthsc.edu
Twitter: @saunaksen
Orcid: 0000-0003-4519-6361