| 21 Jan |
|
Introductory case study   |
| 23 Jan |
|
Reproducible research |
| 28 Jan |
|
Simulations: genomes of recombinant inbred lines |
| 30 Jan |
|
R Markdown |
| 4 Feb |
|
EM algorithm: T cell frequencies |
| 6 Feb |
|
Know the command line; know your editor |
| 11 Feb |
|
EM algorithm: QTL mapping with a cure model |
| 13 Feb |
|
Git and GitHub |
| 18 Feb |
|
Git/GitHub laboratory  |
| 20 Feb |
|
Model misspecification: Estimating allele frequencies |
| 25 Feb |
|
Sample mix-ups in eQTL data |
| 27 Feb |
|
Organizing collaborative 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 |
|
Data visualization |
| 2 Apr |
|
Software testing and debugging |
| 7 Apr |
|
Permutation test with selective genotyping |
| 9 Apr |
|
Big jobs/simulations; caching computations |
| 14 Apr |
|
Building regression models: Multiple-QTL analysis |
| 16 Apr |
|
R Markdown for papers |
| 21 Apr |
|
Dissecting and fine-mapping trans-eQTL hotspots |
| 23 Apr |
|
Containers for reproducibility |
| 28 Apr |
|
Developing, maintaining, and supporting software: R/qtl |
| 30 Apr |
|
Software/data licenses, copyright, and human subjects/HIPAA |