BMI206: Statistical Methods

OVERVIEW – SYLLABUS – READING –  LABS – TUTORIALS – PROJECT

Statistical Analysis Labs

Coding concepts will be introduced on Tuesdays. In-class work is on Thursdays, and the remainder of the lab is homework due Friday.

Collaboration is encouraged, but please write up your own solution (code and exposition).

Turn in your write up of each lab by midnight Friday by email to Prof. Pollard and the TAs. The write up should be a an R markdown (.Rmd) file with code blocks showing your work and text fields with your explanations of what you did, why, and what it means. Your exposition is a key part of the assignment and may also help you to get partial credit even when the final output is not correct. Please confirm that your file compiles, by running knit on it after commenting out eval=FALSE from all code blocks.

Due Date	Topic	Files	To Prepare
Oct 17	Linear models for quantitative genetics	files solution	Download and review files Install the most current version of R on your laptop and get familiar with it Install Jupyter including installing R essentials (details in tutorial)
Oct 24	Genomic enrichment analysis	files solution	Download and review files Read and run through the regioneR vignette
Nov 7	Exploratory data analysis	files solution	Slides-Exploratory Data Analysis Ch7: EDA from R for Data Science EDA: data visualization or torture? Download and review files
Nov 21	Networks and Cytoscape	files solution	Download and review files Install the most current version of Cytoscape on your laptop and get familiar with it Install the Cytoscape app BiNGO Install the R packages plyr, RColorBrewer, and ggplot2
Dec 5	Visualizing single-cell data	files solution	Download and review files Install the R packages Rtsne and Matrix