🧬 Single-Cell Analysis Platform (scRNA-seq)

An end-to-end single-cell RNA sequencing (scRNA-seq) analysis and visualization platform built using FastAPI, Scanpy, and AnnData, supporting real biological datasets (PBMC) with interactive UMAP visualization.

🔍 Overview

This project implements a complete backend pipeline for single-cell transcriptomic analysis, starting from raw count data to dimensionality reduction, clustering, and visualization.

The system is designed as a research prototype, focusing on correctness, reproducibility, and extensibility rather than UI complexity.

🧪 Features Implemented ✅ Data Handling

Load real PBMC scRNA-seq datasets

Support for large sparse gene expression matrices

Automatic cell × gene matrix handling via AnnData

✅ Preprocessing Pipeline

Library size normalization

Log-normalization

Feature scaling

Principal Component Analysis (PCA)

✅ Dimensionality Reduction

UMAP computed on PCA space

Configurable parameters (neighbors, components)

✅ Clustering

Graph-based Leiden clustering

Uses igraph backend

Cluster labels stored in AnnData object

✅ Visualization

Interactive UMAP plot (HTML)

Zoom, pan, hover cell IDs

Cells colored by cluster

Suitable for exploratory biological analysis

🏗️ System Architecture singlecell-platform/ │ ├── backend/ │ ├── app/ │ │ ├── api/ │ │ │ ├── datasets.py # CSV / dataset endpoints │ │ │ ├── umap.py # UMAP + clustering API │ │ │ └── default.py # PBMC loader API │ │ ├── services/ │ │ │ └── singlecell_csv.py │ │ ├── state.py # Global AnnData state │ │ └── main.py # FastAPI app │ └── static/ │ └── umap.html # Interactive UMAP visualization │ └── README.md

🚀 How to Run

1️⃣ Create Environment

python -m venv venv source venv/bin/activate # Windows: venv\Scripts\activate

2️⃣ Install Dependencies pip install fastapi uvicorn scanpy anndata umap-learn igraph plotly

3️⃣ Start Server uvicorn app.main:app --reload

Server runs at: http://127.0.0.1:8000

🧭 API Endpoints Load PBMC Dataset POST /api/load_pbmc

Response { "status": "PBMC loaded", "cells": 2700, "genes": 2000 }

Get UMAP Coordinates GET /api/umap Returns cell-wise UMAP coordinates with cluster labels.

Visualization Open in browser: http://127.0.0.1:8000/static/umap.html

🧠 Research Significance

Implements a standard scRNA-seq analysis workflow

Uses industry-standard tools (Scanpy, AnnData)

Suitable as:

Research prototype

Methods chapter foundation

Base for further biological extensions

🏁 Project Status

✅ Completed — Version 1.0 This version represents a stable, functional, and research-ready implementation.

👤 Author Anurag Lal Software Engineer | Scientific Computing | Research Systems