Using R for Differential Gene Expression (DGE) Analysis

Description:

During this 1.5-day workshop participants can expect to learn the following:

Understand the considerations for performing statistical analysis on RNA-Seq data
Starting with Gene Counts (after alignment and counting), perform basic QC on the count data
Use DESeq2 to perform differential expression (DE) analysis on the count data and obtain a list of significantly different genes
Visualize expression patterns of DE genes
Functional analysis of DGE results

Setup:

This workshop requires you to have Rstudio and R installed on your laptop. You should already have both of these, having previously attended the Intro to R Workshop. Please install the following R packages on the laptop you will be using in class, using the instructions provided below.

Within the RStudio console, use the code below to install the following packages. Note that these package names are case sensitive!

source("http://bioconductor.org/biocLite.R")

biocLite(c("RColorBrewer", "pheatmap", "gProfileR", "DESeq2", "clusterProfiler",

"DOSE", "org.Hs.eg.db", "pathview", "treemap", "purrr", "SPIA", "DEGreport"))

Finally, check that all the packages were installed successfully by loading them:

library(DESeq2)
library(ggplot2)
library(RColorBrewer)
library(pheatmap)
library(clusterProfiler)
library(DEGreport)
library(org.Hs.eg.db)
library(DOSE)
library(pathview)
library(SPIA)
library(purrr)
library(gProfileR)
library(treemap)

Schedule:

******************************** Day1 Schedule********************************
09:00 - 10:00	Overview of DGE Analysis Workflow	Meeta
10:00 - 10:45	Setting up for DGE Analysis: Count Normalization	Radhika
10:45 - 11:00	Coffee
11:00 - 12:30	Setting up for DGE Analysis: Count Data QC	Mary
12:30 - 13:30	Lunch
13:30 - 14:30	Overview of DESeq2 Methods	Mary
14:30 - 15:15	DGE Analysis: Pairwise Comparisons	Meeta
15:15 - 15:30	Coffee
15:30 - 16:30	DGE Results Summarization and Visualization	Radhika

******************************** Day2 Schedule********************************
09:00 - 09:30	DGE Workflow Summary	Mary
09:30 - 10:30	DGE Analysis: Complex Experimental Designs (LRT)	Meeta
10:30 - 11:45	Functional Analysis	Mary
11:45 - 12:00	Wrap-Up	All

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