DGE-Analysis

This is a Differential Gene Expression (DGE) Analysis with DESeq2 using a reference genome.

FILE REQUIREMENTS

• csv file with your raw counts (not-normalized) obtained from a previous Gene Expression Quantification.

• The metadata matrix should contain a column with all your sample names and another column with the corresponding treatment levels (min 2 levels). Here, metadata matrix is built within the DE_Analysis code, so you'll need to adapt that part of your code to your data.

FILE OUTPUTS

• Heatmap DGE-heatmap.png
• Principal Component Analysis DGE-pca.png
• Volcano plot DGE-volcanoplot.png
• Dispersions plot DGE-dispersions.png
• Normalized Results DGE-results.csv
• Shrunk Results DGE-shrunkresults.csv

PACKAGE REQUIREMENTS

Install required libraries from Bioconductor

Run this code if the packages are not already installed

install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install("genefilter")
BiocManager::install("calibrate")
BiocManager::install('MASS')
BiocManager::install('MatrixGenerics')
BiocManager::install('matrixStats')

Load required libraries

# Differential Expression Analysis
library("DESeq2")
# Heatmap
library(RColorBrewer)
library(gplots)
# PCA plot
library(genefilter)
# Volcano plot
library(ggplot2)
library(EnhancedVolcano)