Evo Geno Exercises

Exercises for “Evolutionary Genomics and Bioinformatics” course.

Last updated: December 4, 2020

R Tutorials and Exercises

Corresponding instructions for all labs by Dr. Blanchard here

Lab 1: Intro to R & Markdown || Exercises

Lab 2: Intro to Github & adding references to Markdown || Exercises

Lab 3: Data Wrangling in R || Exercises B

Lab 4: Working with COVID data in R - Part 1 || Exercises, Visualization tutorial (4A)

Lab 5: Working with COVID data in R - Part 2 || Exercises, Visualization tutorial (5A)

Lab 5 extra: Interactive Graphs and Animations | Exercises

Lab 6: Data Maps and Interactive Graphs from the COVID-19 reporting data || Exercises

Lab 6 extra: Shiny Apps

Lab 7: RNA-Seq Workflow: gene-level exploratory analysis and differential expression || Exercises

Lab 7 extra: Working on the Command Line

Lab 8: Sequence Alignment, Phylogenetic Analysis and Tree Visualization || Exercises

Lab 9: Programming in R - Regular Expressions || Exercises

Lab 9 extra: Programming in R - Control Structures and Functions || Exercises

Lab 10: Population genomics based on high throughput sequencing (HTS) || Exercises

Lab 11: Microbiome Analysis using data2 and phyloseq || Exercises

Lab 11 extra: Microbiome Analysis using phyloseq || Exercises

Lab 12: Network Analysis using Cytoscape and RCy3 || Exercises

Lab 13: Sprucing up your Rmarkdown and Github Page || Exercise

Python Tutorials and Exercises

Data Carpentry Instructions

Starting with Data || Exercises

Indexing, Slicing and Subsetting || Exercises

Data Types and Formats || Exercises

Combining DataFrames with Pandas || Exercises

Data Workflows and Automation || Exercises