Welcome to the Single Cell Omics knowledge base repository! This collaborative resource serves as a centralized hub for protocols, analyses, best practices, and documentation related to single-cell genomics research.

🧬 Purpose

This knowledge base aims to:

  • Document standard operating procedures for single-cell experiments
  • Share analysis workflows and code snippets
  • Maintain best practices for data processing and visualization
  • Foster knowledge sharing within the Single Cell Omics community
  • Provide reproducible examples and tutorials

📚 Structure

├── analyses/           # Analysis workflows and examples
├── protocols/          # Laboratory and computational protocols  
├── tutorials/          # Step-by-step guides and tutorials
├── references/         # Literature reviews and method comparisons
├── templates/          # Template .Rmd files for new content
├── assets/            # Images, data files, and other resources
└── _site/             # Generated HTML files (auto-generated)

🚀 Getting Started

For Readers

  • Browse the live knowledge base (GitHub Pages)
  • Navigate through categories using the folder structure above
  • All content is version-controlled and citable via GitHub

For Contributors

  1. Read our Contributing Guide
  2. Fork this repository
  3. Create content using our R Markdown templates
  4. Submit a pull request

🛠️ Technical Details

This knowledge base is built using:

  • R Markdown (.Rmd files) for reproducible documentation
  • GitHub Pages for web hosting
  • GitHub Actions for automated building and deployment
  • HTML output format for web compatibility

Repositories

📝 Content Categories

Analyses

  • Single-cell RNA-seq pipelines
  • Multi-modal data integration
  • Trajectory analysis workflows
  • Quality control procedures

Protocols

  • Cell preparation and isolation
  • Library preparation methods
  • Sequencing guidelines
  • Data management practices

Tutorials

  • Getting started with single-cell analysis
  • Software installation guides
  • Visualization techniques
  • Statistical methods

References

  • Method comparisons
  • Literature reviews
  • Tool evaluations
  • Best practice summaries

🤝 Contributing

We welcome contributions from all members of the Single Cell Omics community! Please see our Contributing Guide for detailed instructions.

Quick contribution steps:

  1. Fork the repository
  2. Create a new branch for your content
  3. Use the provided templates in templates/
  4. Follow our style guide
  5. Submit a pull request

📋 Content Standards

  • All analyses must be reproducible
  • Include session information and package versions
  • Use clear, descriptive titles and headings
  • Provide biological context and interpretation
  • Include references to relevant literature

🔧 Local Development

To work with this repository locally:

# Clone the repository
git clone https://github.com/shd-test/Knowledge-base.git
cd single-cell-omics-kb

# Install required R packages
Rscript -e "install.packages(c('rmarkdown', 'knitr', 'here'))"

# Knit an individual document
Rscript -e "rmarkdown::render('path/to/your/document.Rmd')"

📞 Support

📄 License

This knowledge base is licensed under MIT License - feel free to use, modify, and share!

🏷️ Citation

If you use content from this knowledge base in your research, please cite:

Single Cell Omics Knowledge Base. GitHub repository: 
https://github.com/shd-test/Knowledge-base

Last updated: 2025-06-25 | Contributors: See CONTRIBUTORS.md