Śaunak Sen | Research Group

For statistical methods to have real-world impact they need an implementation so that they can be used. We have developed software in Julia, R and Matlab, although most recent work has been in Julia.

• R/qtlDesign R package for design of QTL (quantitative trait locus) experiments (Saunak Sen, Karl Broman, Jaya Satagopan, Gary Churchill))
• BigRiverQTLPlots.jl Julia package for plots used in genetic analysis such as Manhattan plots and eQTL plots (Gregory Farage)
• BulkLMM.jl Julia package for performing a large number of univariate linear mixed model genome scans; suitable for eQTL analysis and genome scans with high-throughput phenotypes (Zifan Yu, Gregory Farage, Chelsea Trotter, Saunak Sen)
• MetabolomicsWorkbenchAPI.jl Julia interface to Metabolomics Workbench (Gregory Farage)
• GeneNetworkAPI.jl Julia interface to GeneNetwork (Chelsea Trotter, Gregory Farage, Saunak Sen)
• MatrixLMnet.jl Julia package for elastic net penalized matrix linear models (Jane Liang, Gregory Farage, Chenhao Zhao)
• MatrixLM.jl Julia package with core functions for matrix linear models (Jane Liang, Gregory Farage, Chenhao Zhao)
• Helium.jl A fast and flexible Julia tabular serialization format (Gregory Farage)
• GeneticScreens.jl Julia package for analysis of high-throughput genetic screens (Jane Liang)
• FlxQTL.jl Julia package for multivariate LMMs for structured traits (Hyeonju Kim)
• LiteQTL.jl Julia package for eQTL scans using GPUs (Chelsea Trotter)
• FastLMM.jl Julia package for univariate LMMs (Saunak Sen)
• R/lcest R package for estimation for bivariate left-censored data (Emily Hanson)

courses

• BIOE806 - R for Biostatistics - II Second R course (Gregory Farage and Saunak Sen)
• BIOE805 - R for Biostatistics - I Introductory R course (Gregory Farage and Saunak Sen)
• BIOE720 - Biostatistics for Public Health Introductory Biostatistics using Stata

workshops and webinars

• An Introduction to Julia for Biostatistics Materials for ENAR 2023 workshop on 2023-03-19 in Nashville, TN (Gregory Farage and Saunak Sen)
• Julia introductory workshop Materials from a workshop at UTHSC on 2029-10-25 introducing Julia (Gregory Farage, Chelsea Trotter and Saunak Sen)
• Webinar Series - Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions Webinar series organized by the NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome (Saunak Sen, Laura Saba, Rob Williams and others); includes videos and supplementary interactive notebooks

We have developed several interactive notebooks using Julia. These can be used as reactive applications, and can also be optionally modified and run on Binder. The notebooks are hosted by the GeneNetwork project.

diagnostic tests

• Diagnostic tests: prevalence, sensitivity, specificity, and predictive values How the postive/negative predictive values of a diagnostic test based on a quantitative measurement behave.
• Diagnostic test with a varying cutoff Shows how varying the cutoff point for a quantitative diagnostic test can affect sensitivity and specificity.

probability and simulations

• Coin flip simulator Simulates what would happen if you flipped a coin a bunch of times, and kept a running tally of the proportion of heads.
• Common distributions Simulator of common probability distributions as you vary the parameters of those distributions.
• Central Limit Theorem Illustrates the Central Limit Theorem by visualizing the histogram of the sample mean for different distribution and sample sizes.
• Probability rules and Bayes Theorem Graphical illustration of Bayes Theorem.

power and sample size

• How power depends on effect size, sample size, and the desired false positive rate Interactive visualization of impact of effect size and sample size on power.

optimization techniques

• How the L1-penalty achieves sparsity Illustration of how minimizing a quadratic loss function with an L1 penalty helps acheive sparsity.
• How the proximal operator works Illustration of the proximal operator used in optimization.

As a computationally oriented research group, we try to be as transparent as possible. A big part of that is to make software and code used in our papers public.

• Gregory Farage and others Connecting metabolite composition to individual characteristics
• Timothy J. Garrett and others Effect of Statin Treatment on Metabolites, Lipids and Prostanoids in Patients with Statin Associated Muscle Symptoms (SAMS)
• Suheeta Roy and others Gene-by-environment modulation of lifespan and weight gain in the murine BXD family
• Chelsea Trotter and others Speeding up eQTL scans in the BXD population using GPUs
• Gregory Farage and others Assessing the contribution of self-monitoring through a commercial weight loss app: mediation and predictive modeling
• Jane Liang and others Matrix linear models for high-throughput chemical genetic screens
• Jane Liang and Saunak Sen Sparse matrix linear models for structured high-throughput data
• Mao and others Identification of fibronectin1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome
• Hao Xiong and Saunak Sen A flexible estimating equations approach for mapping function-valued traits
• Saunak Sen and others Selective genotyping and phenotyping strategies in a complex trait context
• Saunak Sen and others Quantitative trait locus study design from an information perspective

R/qtlCurve on Bitbucket

The package implements methods described in

---

Xiong H, Goulding EH, Carlson EJ, Tecott LH, McCulloch CE, Sen S.
A flexible estimating equations approach for mapping function-valued traits.
Genetics. 2011 Sep; 189(1):305-16

---

R/qtl website

---

A guide to QTL mapping with R/qtl
Karl W. Broman and Śaunak Sen
Springer, 2009

---