Evolutionary Genomics and Bioinformatics - FA20

This is rendering html files from the course repository (https://github.com/jeffreyblanchard/evogeno) for Evolutionary Genomics & Bioinformatics taught at the University of Massachusetts Amherst in Fall 2020 by Prof. Jeffrey Blanchard

Labs

R Basics

• 1 : Introduction to R and Reproducible Research
• 2 : git, GitHub and Rstudio project
• 5.1 : Data visualization with ggplot2
• 5.2 : Lab5 Exercises
• 5.extra : Interactive Graphs and Animations from the COVID-19 reporting data
• 6 : Data Maps and Interactive Graphs from the COVID-19 reporting data
• 6-Report : REPORT ON LATEST US COVID19 STATISTICS
• 6-Shiny : R Shiny apps using the COVID-19 reporting data
• 7 : RNA-Seq workflow: gene-level exploratory analysis and differential expression
• 8 : Sequence Alignment, Phylogenetic Analysis and Tree Visualization
• 9 : Programming in R - Regular Expression
• 9x : Programming in R - Control Structures and Functions
• 10 : Population genomics based on high throughput sequencing (HTS)
• 11 : Microbiome Analysis using dada2 and phyloseq
• 11x : Microbiome Analysis using phyloseq
• 12 : Network Analysis using Cytoscape and RCy3

Python Basics

• 3.2 : Short Introduction to Programming in Python
• 3.3 : Starting with Data
• 3.4 : Indexing, Slicing and Subsetting DataFrames in Python
• 4.1 : Data Types and Formats
• 4.2 : Combining DataFrames and Pandas
• 4.3 : Data Workflows and Automation
• 4.4 : Making Plots with plotnine
• 5.1 : Data Ingest and Visualization - Matplotlib and Pandas
• 5.2 : Accessing SQLite Databases Using Python and Pandas