Celline - Single Cell RNA-seq Analysis Pipeline

Celline is a comprehensive, interactive pipeline for single-cell RNA sequencing (scRNA-seq) analysis, designed to streamline the workflow from raw data to biological insights. It provides both command-line and web-based interfaces for flexible analysis workflows.

📖 Detailed Documentation: Celline Docs

Features

• 🔄 Automated Data Processing: From raw FASTQ files to expression matrices
• ✅ Quality Control: Built-in QC metrics and filtering with Scrublet doublet detection
• 📊 Dimensionality Reduction: PCA, t-SNE, and UMAP implementations
• 🔍 Clustering Analysis: Multiple clustering algorithms
• 🧬 Cell Type Prediction: Automated cell type annotation using scPred
• ⚖️ Batch Effect Correction: Multiple methods for data integration (Seurat, scVI)
• 🌐 Interactive Visualization: Web-based interface for data exploration
• 🔧 Flexible Execution: Support for local multithreading and PBS cluster execution
• 📁 Database Integration: Built-in support for SRA, GEO, and CNCB data repositories
• 🔬 R Integration: Seamless R/Seurat integration for advanced analysis

System Requirements

Required Dependencies

• Python: ≥3.10
• R: ≥4.0 with Seurat and other required packages
• Cell Ranger: For 10x Genomics data processing
• SRA Toolkit: For downloading SRA data (fastq-dump)

Python Dependencies

All Python dependencies are automatically installed via pip. Key packages include: - scanpy - Single-cell analysis - pandas, polars - Data manipulation - fastapi, uvicorn - Web API - rich - Enhanced CLI interface - pysradb - SRA database access

Installation

Option 1: Install from PyPI

bash pip install celline

Option 2: Install from Source

bash git clone https://github.com/your-repo/Celline.git cd Celline pip install -e .

Option 3: Development Installation

bash git clone https://github.com/your-repo/Celline.git cd Celline pip install -e ".[dev]"

Quick Start

1. Initialize Your Project

Start by initializing a new project. This will validate system dependencies and create configuration files:

bash celline init

This command will: - Check for required system dependencies (R, Cell Ranger, SRA Toolkit) - Set up R environment configuration - Create project configuration files - Prompt for project name and settings

2. Configure Execution Settings (Optional)

Configure execution parameters for your system:

```bash

Interactive configuration

celline config

Or set specific options

celline config --system multithreading --nthread 8 celline config --system PBS --pbs-server your-cluster-name ```

3. Explore Available Functions

List all available analysis functions:

bash celline list

Get detailed help for specific functions:

bash celline help download celline help preprocess

4. Basic Analysis Workflow

Download Public Data

```bash

Download from SRA/GEO

celline run download --accession GSE123456 celline run download --accession SRR123456

Download from CNCB

celline run download --accession CRA123456 ```

Data Preprocessing

```bash

Quality control and preprocessing

celline run preprocess --input raw_data/ --output processed/

Gene expression counting (10x data)

celline run count --input cellranger_output/ --output counts/ ```

Create Seurat Objects

```bash

Create Seurat object for downstream analysis

celline run createseurat --input counts/ --output seuratobject.rds ```

Advanced Analysis

```bash

Dimensionality reduction

celline run reduce --input seurat_object.rds --methods pca,umap,tsne

Cell type prediction

celline run predictcelltype --input seuratobject.rds --reference ref_data/

Batch effect correction

celline run integrate --input multiple_samples/ --method seurat ```

5. Interactive Web Interface

Launch the interactive web interface for visual analysis:

bash celline interactive

This will: - Start the FastAPI backend server - Launch the Vue.js frontend - Open your web browser automatically - Provide interactive data exploration tools

6. API Server Only (for Development)

Start only the API server for testing:

bash celline api

Available Functions

| Function | Description | Usage Example | |----------|-------------|---------------| | init | Initialize project and validate dependencies | celline init | | download | Download scRNA-seq data from public repositories | celline run download --accession GSE123456 | | preprocess | Quality control and preprocessing | celline run preprocess | | count | Gene expression quantification | celline run count | | create_seurat | Create Seurat objects | celline run create_seurat | | reduce | Dimensionality reduction (PCA, UMAP, t-SNE) | celline run reduce | | integrate | Batch effect correction and data integration | celline run integrate | | predict_celltype | Automated cell type annotation | celline run predict_celltype | | batch_cor | Batch correlation analysis | celline run batch_cor | | interactive | Launch web interface | celline interactive | | sync_DB | Update local databases | celline run sync_DB | | info | Show system information | celline info |

Project Structure

When you initialize a project, Celline creates the following structure:

your_project/ ├── setting.toml # Project configuration ├── data/ # Raw and processed data ├── results/ # Analysis results ├── scripts/ # Generated analysis scripts └── logs/ # Execution logs

Configuration

Celline uses setting.toml files for configuration:

```toml [project] name = "my_project" version = "0.01"

[execution] system = "multithreading" # or "PBS" nthread = 8 pbs_server = "your-cluster" # for PBS system

[R] r_path = "/usr/local/bin/R"

[fetch] wait_time = 4 # seconds between API calls ```

Advanced Usage

Running on HPC Clusters

For PBS/Torque clusters:

bash celline config --system PBS --pbs-server your-cluster-name celline run preprocess # Will submit PBS jobs automatically

Custom Analysis Scripts

Celline generates executable scripts in the scripts/ directory that can be run independently or modified for custom workflows.

R Integration

Access Seurat objects and run custom R analysis:

```bash

R scripts are available in template/hook/R/

Custom R functions can be added to the pipeline

```

Troubleshooting

Common Issues

1. Missing Dependencies: Run celline init to validate all dependencies
2. R Package Issues: Ensure Seurat and required R packages are installed
3. Memory Issues: Adjust thread count with celline config --nthread <number>
4. Web Interface Not Loading: Check that ports 8000 and 3000 are available

Getting Help

```bash

General help

celline help

Function-specific help

celline help

System information

celline info

List all functions

celline list ```

Contributing

We welcome contributions! Please see our contributing guidelines for more information.

Citation

If you use Celline in your research, please cite:

[Citation information to be added]

License

This project is licensed under the MIT License - see the LICENSE file for details.

Support

• 📖 Documentation
• 🐛 Issue Tracker
• 💬 Discussions