This is rendering hmtl files from the course repository (https://github.com/jeffreyblanchard/GenomeAnalysisR) for Human Genome Analysis in R taught at the University of Massachusetts Amherst in Spring 2020 by Prof. Jeffrey Blanchard

Labs

R Basics

• 1 : Introduction to R and Reproducible Research
• 2 : Basic R Object types and Producing Reports With knitr

The R Tidyverse

• 3 : Graphics with ggplot2
• 4 : Publication Graphics
• 5 : Data Wrangling
• 6 : Github and Collaborative Projects

RNA-seq Analysis

• 7 : Data Preprocessing and Normalization

Genealogies

• 8 : Genealogical Trees

COVID-19 reporting data and SARS-CoV-2 genome analysis

• 9 : Working with the COVID-19 data reporting from GitHub
• 10 : More Geographical Maps, Interactive Graphs and Animations from the COVID-19 reporting data
• 11 : R Shiny apps using the COVID-19 reporting data
• 12 : More on R Shiny apps using the COVID-19 reporting data

Students taking 697 will be expected to complete these following additional labs

• 13 : Project Organization and Management
• 14 : The Command Line
• 15 : Accessing High Performance Computers
• 16 : Assessing Read Quality
• 17 : Trimming and Filtering

• 18 : Read Mapping - Variant Calling Workflow

• 19 : Integrating COVID-19 reporting and US Census data