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