RNA-Seq Analysis

Overview

This repository contains an R script for performing RNA-Seq data analysis, including data preprocessing, differential expression analysis, visualization, and functional enrichment. The script utilizes popular R packages such as edgeR, limma, and org.Mm.eg.db for efficient and comprehensive analysis.

---

Features

1. Data Preprocessing

• Reads count data and sample information.
• Filters low-expressed genes and normalizes counts.

2. Exploratory Data Analysis

• Library size bar plots.
• Multidimensional scaling (MDS) plots.
• Heatmaps of highly variable genes.
• Boxplots of log CPM values.

3. Differential Expression Analysis

• Linear modeling using voom from limma.
• Generalized linear models (GLM) using edgeR.
• Identification of significant differentially expressed genes (DEGs).

4. Visualization

• MD plots for DEGs.
• Heatmaps of top DEGs.
• Venn diagrams for comparison of conditions.

5. Functional Enrichment

• Gene Ontology (GO) analysis.
• KEGG pathway analysis.
• Top enriched pathways and biological processes.

---

Dependencies

The following R packages are required to run the script:

• edgeR
• limma
• org.Mm.eg.db
• RColorBrewer
• gplots
• tidyverse

To install these packages, run:

install.packages(c("RColorBrewer", "gplots", "tidyverse"))
BiocManager::install(c("edgeR", "limma", "org.Mm.eg.db"))