SC-Framework

The SC-Framework is a single-cell analysis platform designed for reproducible, flexible, and guided workflows across multiple modalities. Built as a FAIR-compliant, layered, semi-interactive environment, it combines a robust Python package with a series of structured Jupyter Notebooks to streamline RNA and ATAC sequencing analysis. The framework automatically sets up organized directory structures, generates visualizations, tables, and log files, and ensures traceability through self-documenting data objects. With containerized releases, the SC-Framework supports reproducibility on local systems and high-performance computing clusters—making it ideal for collaborative, scalable, and long-term single-cell research. Read the paper to find out more.