Sen Research Group Resources
Software
- 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)
Teaching resources
- BIOE805 - R for Biostatistics - I Introductory R course (Gregory Farage and Saunak Sen)
- BIOE806 - R for Biostatistics - II Second R course (Gregory Farage and Saunak Sen)
- BIOE720 - Biostatistics for Public Health Introductory Biostatistics using Stata
- Julia introductory workshop Materials from a workshop 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)
Interactive visualizations
These use Julia’s Pluto notebooks.
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.