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

Interactive visualizations

These use Julia’s Pluto notebooks.

Diagnostic tests

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

Optimization techniques