RNA-Seq Analysis with DESeq2

This repository contains the script and data required for RNA-Seq differential expression analysis using the DESeq2 package in R. The script guides you through the steps of data preprocessing, normalization, and differential expression analysis.

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Contents

1. RNA_sequencing.Rmd - R Markdown script for RNA-Seq analysis.
2. /data/ - Folder containing input data files:
   • raw_counts.csv: Raw count matrix (genes × samples).
   • metadata.csv: Metadata for samples, including experimental conditions.

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Requirements

Software

• R (version ≥ 4.0)
• RStudio (optional, for easier execution)

R Packages

The following R packages are required:

• tidyverse
• DESeq2
• ggplot2
• plotly
• GenomicRanges
• mixOmics

Install these packages using the following commands in R:

install.packages(c("tidyverse", "ggplot2", "plotly"))

# Install Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install(c("DESeq2", "GenomicRanges", "mixOmics"))

Clone this Repository:

git clone https://github.com/your-username/RNA_Seq_Analysis.git
cd RNA_Seq_Analysis