COVID-19: For the rest of the semester, lectures and office hours will be strictly online. More information here.

Date      Topic/Reading
21 Jan   Introductory case study pdf icon notes icon
23 Jan   Reproducible research pdf icon notes icon
28 Jan   Simulations: genomes of recombinant inbred lines pdf icon notes icon
30 Jan   R Markdown pdf icon notes icon
4 Feb   EM algorithm: T cell frequencies pdf icon notes icon
6 Feb   Know the command line; know your editor pdf icon notes icon
11 Feb   EM algorithm: QTL mapping with a cure model pdf icon notes icon
13 Feb   Git and GitHub pdf icon notes icon
18 Feb   Git/GitHub laboratory html icon pdf icon
20 Feb   Model misspecification: Estimating allele frequencies pdf icon notes icon
25 Feb   Sample mix-ups in eQTL data pdf icon notes icon
27 Feb   Organizing collaborative projects; capturing exploratory analysis pdf icon notes icon
3 Mar   Data diagnostics for multiparent populations pdf icon notes icon
5 Mar   Writing clear code pdf icon notes icon
10 Mar   Bayes/MCMC: Transposon mutagenesis pdf icon notes icon
12 Mar   Wrangling messy data files pdf icon notes icon
17,19 Mar   No class (spring break)
24 Mar   Bootstrap confidence intervals for QTL location pdf icon notes icon html icon video icon
26 Mar   Writing R packages; roxygen2 pdf icon notes icon html icon video icon
31 Mar   Data visualization pdf icon notes icon video icon
2 Apr   Software testing and debugging pdf icon notes icon video icon
7 Apr   Permutation test with selective genotyping pdf icon notes icon video icon
9 Apr   Big jobs/simulations; caching computations pdf icon notes icon video icon [homework 3 due]
14 Apr   Building regression models: Multiple-QTL analysis
16 Apr   R Markdown for papers
21 Apr   Fine-mapping an eQTL
23 Apr   Containers for reproducibility
28 Apr   Developing, maintaining, and supporting software: R/qtl
30 Apr   Software/data licenses, copyright, and human subjects/HIPAA