WELCOME
Integrated Bioanalytics documents methods for analyzing chemical and sequence data in R as well as some basics of scientific writing. It is maintained by Lucas Busta and members of the Busta lab. To run the analyses described in this book you will need to run a source script that will set up your R environment with a variety of packages, custom functions, and datasets. If you don’t have R, see “installation” under “Data Analysis In R” in the table of contents. Run the source script by pasting and executing the following in your R command line (RStudio recommended). If you are in the Busta Lab (or want access to full features), define an object bustalab = TRUE before running the source command. If you have trouble running the source script, please reach out to Lucas Busta at: bust0037@d.umn.edu. The source script:
source("https://thebustalab.github.io/phylochemistry/phylochemistry.R")Features provided by the source script:
–Analysis and visualization tools–
- A GC-MS data analysis application with a MS reference library.
- A sequence alignment analysis application for trimming alignments.
- BLAST searches that export .fasta files of hits and store results in a .csv file.
- Functions for dimensionality reduction, clustering, modeling, and visualization.
–Useful data and data structures–
- More than 12 chemical data sets for running practice analyses.
- A phylogeny for >30,000 plant species, including nearly 30,000 angiosperms, >500 gymnosperms, nearly 500 pteridophytes, and 100 bryophytes (https://thebustalab.github.io/data/plant_phylogeny.newick).
- A list of nearly 400,000 plant species as well as the families, orders, and phyla to which they belong (https://thebustalab.github.io/data/plant_species.csv).
- Support for multiple column and row names.