R Cookbook
The R Cookbook, developed by Colleen Nell, Kailen Mooney, and John Powers, gives a framework for answering scientific questions in R through data visualization and linear models. It covers getting started in R, troubleshooting, organizing and importing data, generating summary statistics, picking an appropriate model for your experimental design, and plotting boxplots, barplots, and scatterplots. Developed for UCI’s Field Biology course but useful for any beginners to data analysis and statistics with R.
Data Visualization in R
A set of slides for teaching the basics of data visualization, and ggplot2 basics.
Filtering GC-MS datasets
The R package bouquet has been developed by Katherine Eisen, John Powers, Diane Campbell, and Robert Raguso to provide a flexible and reproducible pipeline to filter large GC-MS datasets, with application to biological samples such as plant and floral volatiles. It works by comparing the levels of each compound in samples and controls, and applying other filters based on retention time, rarity, maximum area, and manual exclusions. It can generate diagnostic plots of the filtering process. Planned functionality includes importing data from PubChem, the Pherobase, and SCENTbase to augment the dataset, and . You can install it from Github via the remotes package:
remotes::install_github("jmpowers/bouquet", build_vignettes=T)
The bouquet package is now published!