This repository contains materials from a course that I taught in the Department of Crop Sciences at the University of Illinois, Urbana-Champaign in the fall of 2018. I won't be teaching the course anymore since I am changing jobs, but I wanted to make the materials available.
Every week there was a Tuesday lecture (supplied as a PDF, often with R files from the live coding that I did in class) and a Thursday lab (supplied as HTML and Rmd files).
I'm not redistributing genome sequence and annotation files in this repository since I'm pretty sure I don't have the rights to do so, but all are available on Phytozome. You will need to make a free account there. Then select the appropriate organism and go to "Bulk Data" to download the files.
HTML files won't display nicely directly from GitHub. I recommend downloading the repository to your own computer. Then, simply double-click an HTML file to view it in your browser.
- Week 1: Introduction to R and RStudio
- Week 2: If/else, loops, and functions
- Week 3: Graphics
- Week 4: Text processing
- Week 5: Reading and writing files
- Week 6: Matrices, arrays, lists, and apply functions
- Week 7: Environments, data types, and classes
- Week 8: Version control and documentation
- Week 9: Midterm exam, and building an R package
- Week 10: Making your code run faster
- Week 11: Object-oriented programming
- Week 12: Introduction to Bioconductor
- Week 13: Differential expression analysis
- Week 14: Variant calling
- Week 15: Genome-wide association analysis and genomic selection
In several cases, demo data come from a yield trial of Miscanthus sinensis:
Clark, Lindsay V.; Dwiyanti, Maria Stefanie; Anzoua, Kossonou G.; Brummer, Joe E.; Ghimire, Bimal Kumar; Głowacka, Katarzyna; Hall, Megan; Heo, Kweon; Jin, Xiaoli; Lipka, Alexander E.; Peng, Junhua; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P.; Sacks, Erik J. (2019): Miscanthus sinensis multi-location trial: phenotypic analysis, genome-wide association, and genomic prediction . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0790815_V3
Swirl is an interactive tutorial that you can run right from RStudio.
The Carpentries run two-day workshops on a variety of coding and data analysis topics. We have a very active team at UIUC who run workshops regularly, or if you are at another institution you can put in a request for a workshop.
I am currently producing some YouTube videos on coding with R and Python as part of an NSF project.