GenomeAnalysisR

This is a repository for .Rmd and other files for the course Human Genome Analysis in R taught at the University of Massachusetts Amherst in Spring 2020 by Prof. Jeffrey Blanchard

The Github page with rendering of the html files is at https://jeffreyblanchard.github.io/GenomeAnalysisR/

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
• 8 : Data Exploration
• 9 : Differential Expression
• 10 : Genome Visualization
• 11 : Gene Ontology Analysis
• 12 : Network Analysis

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

• 13 : Project Organization and Management
• 14 : The Command Line
• 15 : Working on the MGPCC computers
• 16 : Assessing Read Quality
• 17 : Trimming and Filtering
• 18 : Read Mapping - Variant Calling Workflow
• 19 : Read Mapping - Transcript Counts Workflow