Seurat Single-Cell RNA-seq Analysis Pipeline This repository provides a complete, modular pipeline for analyzing single-cell RNA sequencing (scRNA-seq) data using the Seurat package in R. The pipeline includes quality control, normalization, dimensionality reduction, clustering, differential expression, and visualization, tailored for exploratory and publication-ready analysis.

🔧 Requirements R (≥ 4.0) Seurat (v4+) Tidyverse patchwork Matrix cowplot Install dependencies in R: install.packages("Seurat") install.packages("tidyverse") install.packages("patchwork") install.packages("cowplot") Or use an R environment manager like renv or Conda (environment.yml provided if applicable).

🚀 Usage Clone the repository cd Load your data

Run the pipeline step-by-step Execute each R script in order or combine them in an RMarkdown notebook.

Outputs Plots (UMAP, feature plots, violin plots) Tables (marker genes, QC stats) Final annotated Seurat object for downstream use