The teaching modules we provide here are of the statsTeachR format. statsTeachR is an open-access, online repository of modular lesson plans, a.k.a. "modules", for teaching statistics using R at the undergraduate and graduate level. Each module focuses on teaching a specific statistical concept. The modules range from introductory lessons in statistics and statistical computing to more advanced topics in statistics and biostatistics.
Here, we focus on the analysis of genomic data and extend the statsTeachR framework by giving users the option to open the labs directly in their web browser as well as download the entire module (sample displayed below). Each lesson is comprised of multiple modules pertaining to the given topic. Each module then can contain slides, labs, assignments, quizes and source files for everything in the module. The intention is that users can simply open the PDF form of each element, or they can open the .Rnw file into their R console and manipulate code directly. All modules will also be available on the statsTeachR website.
The GWAS lesson, for example, is broken down into four modules, each containing multiple labs and slides. The first module pertains to what we've termed data-preprocessing, and covers topics ranging from reading genetic data into R to data filtering processes. The remaining modules cover other topics like genotype imputation, association analyses and post-analytic interrogation of results. While the labs cover the same material as the tutorial, the labs are intended to break the code up even further as well as integrate exercises and On Your Own exercises for further understanding. For demonstrative purposes, a portion of the second data-preprocessing lab is displayed below.