RNA-seq Data Analysis with DEGA, EA and GSEA

author: Nicholas Küng
contact: nicholas.kueng@extern.insel.ch

This script uses the Salmon quantification output, a samplesheet file and a gene annotation file to perform:

• Exploratory Data Analyis with a sample correlation and sample distance heatmap, and a PCA plot,
• Differential Expression Analysis,
• GO Enrichment Analysis and
• Gene Set Enrichment Analysis

To run the program and save the output define your working directory. The path has to be entered in line 34 as following:
wddir = "yourPATH/"

In this directory the following files and subdirectories should exist:

• sample specific Salmon output files with quant.sf files
• sample.txt
• salmon_tx2gene.tsv

see Salmon_QuantFiles

Dependencies

• tximport
• RColorBrewer
• DESeq2
• ggplot2
• ggrepel
• pheatmap
• clusterProfiler
• enrichplot
• org.Hs.eg.db
• vsn
• biomaRt
• DEGreport