Getting Started

This is a complete guide to getting started with single-cell RNA-seq analysis using Celline. This section provides step-by-step instructions from installation to your first analysis.

📋 Prerequisites

Before using Celline, please ensure you meet the following requirements:

System Requirements

Python: 3.10 or higher
R: 4.0 or higher (Seurat package required)
Memory: 8GB or more recommended
Storage: Sufficient capacity according to project size

Recommended Tools (Optional)

Cell Ranger: For 10x Genomics data processing (7.0 or higher)
Docker: For reproducible environment setup
Git: For version control

🚀 Installation

Installation via pip

      # Install the latest version
pip install celline

# Install a specific version
pip install celline==0.1.10

Installation in UV Environment

      # Execution in UV environment
uv add celline

# Or execute directly via UV
uv run --with celline celline --help

Development Version Installation

      # Install development version from GitHub
pip install git+https://github.com/YUYA556223/celline.git

⚙️ Initial Setup

1. Project Initialization

      # Start a project in a new directory
mkdir my-scrna-project
cd my-scrna-project

# Initialize Celline project
celline init

2. Configuration Check

      # Check available functions
celline list

# Check system information
celline info

# Check and modify settings
celline config

📁 Project Structure

After initialization, the following directory structure is created:

      my-scrna-project/
├── setting.toml         # Project configuration
├── samples.toml         # Sample information
├── data/                # Analyzed data
├── resources/           # Raw data and metadata
├── results/             # Result files
└── integration/         # Integrated analysis results

🔧 Configuration Files

setting.toml

Manages the overall project configuration:

      [project]
name = "my-scrna-project"
version = "1.0.0"
description = "Single cell RNA-seq analysis project"

[execution]
system = "multithreading"  # or "PBS"
nthread = 4
pbs_server = ""

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

[fetch]
wait_time = 4

samples.toml

Manages information about samples to be analyzed:

      # Samples are automatically added by the celline run add command
GSM1234567 = "Sample 1 description"
GSM1234568 = "Sample 2 description"

🎯 Basic Workflow

Step 1: Add Samples

      # Add samples from GEO
celline run add GSE123456

# Add multiple samples at once
celline run add GSM1234567 GSM1234568

# Add samples from file
celline run add --from-file samples.txt

Step 2: Data Download

      # Download data for added samples
celline run download

# Parallel download (4 threads)
celline run download --nthread 4

Step 3: Count Processing

      # Count processing with Cell Ranger
celline run count

Step 4: Preprocessing

      # Quality control and preprocessing
celline run preprocess

# Target specific cell types only
celline run preprocess --target-celltype Neuron Astrocyte

Step 5: Interactive Analysis

      # Launch web interface
celline interactive

🌐 Execution Modes

CLI Execution

      # Standard CLI execution
celline run [function_name] [arguments]

# Display help
celline help [function_name]

UV Execution

      # Execution in UV environment
uv run celline run [function_name] [arguments]

# Execute with project-specific dependencies
uv run --with celline --with scanpy celline run preprocess

Python Execution

      from celline import Project
from celline.functions.add import Add
from celline.functions.download import Download

# Create project
project = Project("./my-project")

# Add samples
add_samples = Add([Add.SampleInfo(id="GSM1234567", title="Sample 1")])
project.call(add_samples)

# Download data
download = Download()
project.call(download)

⚡ Quick Start Example

Here's an example of a complete workflow:

      # 1. Create project
mkdir test-project && cd test-project
celline init

# 2. Add samples (example: GSE115189)
celline run add GSE115189

# 3. Download data
celline run download --nthread 2

# 4. Count processing
celline run count

# 5. Preprocessing
celline run preprocess

# 6. Start interactive analysis
celline interactive

🔍 Verification and Troubleshooting

Installation Verification

      # Verify Celline is properly installed
celline --help

# Check version
python -c "import celline; print(celline.__version__)"

Common Issues

R packages not found

      # Set R path
celline config --system multithreading

Parallel processing configuration

      # Adjust thread count
celline config --nthread 4

Memory shortage
- Change to fewer threads
- Run with smaller sample sizes

📚 Next Steps

Installation - Detailed installation guide
Quick Start - Complete tutorial
CLI Reference - Command-line details
Configuration - Detailed configuration

Tip: Once setup is complete, check the available commands in CLI Reference.