Guide for the Differential Expression Analysis of RNAseq data using edgeR

Made by David Requena (drequena@rockefeller.edu).

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This code includes some basic steps:

1. SET UP:

• Install and/or call the required libraries
• Input sample metadata

2. Exploring the data:

• Steps available in my previous guide: https://github.com/SimonLab-RU/DEseq2

3. Data Analysis:

• Model matrix
• Prior filtering
• Comparison

4. Plots

To run this script, three tables are required:

• A table with the samples' data, containing features of interest (e.g. cases/controls, gender, etc...)
• A table with the gene counts by sample
• A table with genes to be filtered out (e.g. ribosomal genes)