ScarfWeb
Browser-based single-cell analysis on Scarf. Guides for import, QC, clustering, interpretation, sharing, and platform operations.
Welcome to Nygen docs
Nygen helps research teams move from raw single-cell data to decision-ready biological insight. These docs cover ScarfWeb for browser-based analysis and CyteType for evidence-backed cell annotation, plus the open tools behind the stack.
Product documentation
CyteType
AI-powered cell type annotation with ontology mapping, evidence trails, and report modules your biology team can review.
Built in the open
Open-source engines and open-access tools you can inspect, cite, and build on.
Scarf Open source
A memory-efficient Python library for large-scale single-cell analysis, built on sparse data structures that keep matrices out of RAM. Scarf underpins ScarfWeb clustering, embedding, and downstream assays.
CyteType Open access
An evidence-based cell type annotation workflow that maps clusters to ontology terms, surfaces marker-level support, and returns reviewable report modules for biology teams.
CyteOnto Open source
A utility for automated semantic comparison of cell type annotations against the Cell Ontology, helping quantify agreement and resolve label mismatches across datasets.
Changelog
Recent product and documentation updates.
