DGE workshop
- Khetani, Radhika S.
- Vial6cement!
- Meeta Mistry (Unlicensed)
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
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 | Meeta | |
10:00 - 10:45 | Radhika | |
10:45 - 11:00 | Coffee | |
11:00 - 12:30 | Mary | |
12:30 - 13:30 | Lunch | |
13:30 - 14:30 | Mary | |
14:30 - 15:15 | Meeta | |
| 15:15 - 15:30 | Coffee | |
15:30 - 16:30 | Radhika | |
| ********************************** Day2 Schedule********************************** | ||
|---|---|---|
09:00 - 09:30 | Mary | |
09:30 - 10:30 | Meeta | |
| 10:30 - 11:45 | Functional Analysis | Mary |
| 11:45 - 12:00 | Wrap-Up | All |
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