celline 0.1.6

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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.

Features

• Automated Data Processing: From raw fastq files to expression matrices
• Quality Control: Built-in QC metrics and filtering
• Dimensionality Reduction: PCA, t-SNE, and UMAP implementations
• Clustering Analysis: Multiple clustering algorithms
• Cell Type Prediction: Automated cell type annotation
• Batch Effect Correction: Multiple methods for data integration
• Interactive Visualization: Web-based interface for data exploration
• Reproducible Workflows: Containerized environments and version control

Installation

Install Celline using pip:

pip install celline

Quick Start

After installation, you can use the celline command globally:

# Initialize a new project
celline init

# List available functions
celline list

# Run preprocessing
celline run preprocess

# Launch interactive interface
celline interactive

Documentation

For detailed documentation, please refer to the user guide and API reference.

License

This project is licensed under the MIT License.