Auto_Limma 🧬

A robust, automated R wrapper for Differential Expression Analysis (DEA) based on the Limma workflow.

📖 Introduction

Auto_Limma is designed to streamline the transcriptomic analysis pipeline. Instead of manually constructing design matrices and contrast matrices for every project, this tool encapsulates the standard limma workflow into a single, reusable function.

It handles the statistical modeling (Linear Models & Empirical Bayes) and automatically categorizes genes based on user-defined thresholds.

✨ Key Features

• ⚡ Automated Matrix Construction: Automatically generates model.matrix and makeContrasts based on group factors.
• 🛡️ Robust Statistics: Utilizes eBayes (Empirical Bayes) to moderate standard errors, ensuring reliable results even with small sample sizes (e.g., TCGA rare tumors).
• 🏷️ Smart Tagging: Automatically categorizes genes into UP, DOWN, or NOT significant based on logFC and P-value cutoffs.
• 📊 Output Ready: Produces a clean data frame ready for visualization (Volcano plots, Heatmaps).

🛠️ Dependencies

The script automatically checks for dependencies. If not present, it will attempt to install:

• limma (Bioconductor)

🚀 Usage

1. Clone the repository

git clone [https://github.com/0609x/Auto_Limma.git](https://github.com/0609x/Auto_Limma.git)