CyteType docs
Installation, annotation workflows, report modules, and interpretation guidance for CyteType.
Getting started
- Prerequisites Data and environment requirements before you run CyteType annotation.
- Installation Install the CyteType Python or R client for your annotation workflow.
- First annotation Run a minimal end-to-end CyteType annotation in Python or R.
- How CyteType works The structured multi-agent annotation workflow, artifacts, and data flow.
Running an annotation
Reading the report
- Understanding your report How CyteType report modules fit together when you review annotations.
- Ontology-anchored annotation How CyteType maps each cluster to a Cell Ontology term with confidence and label match.
- Functional state resolution How CyteType separates functional programs such as activation or ECM remodeling from cell type labels.
- Coarse lineage map How CyteType groups clusters into major lineages for first-pass orientation.
- Marker-level evidence How to read supporting, missing, and unexpected genes behind each CyteType call.
- Confidence and heterogeneity QC How to interpret CyteType confidence badges and mixed-cluster heterogeneity signals.
- Multi-expert synthesis How specialized CyteType reviewers agree, disagree, and surface alternative labels.
- Study-aware context How study_context shapes CyteType labels for tissue, disease, and experimental framing.
- Ranked pathway signals How to use GO and WikiPathways enrichment ranked by NES in CyteType reports.
- Linked citations trail How CyteType links gene claims to PubMed citations for verification and audit.
- Decision traceability How to inspect accepted and rejected cell-type candidates behind a CyteType call.
- Interactive Cluster Copilot Ask cluster-specific biology questions grounded in CyteType expression and pathway context.
- Audit-ready export Export CyteType annotation tables for downstream analysis and regulatory documentation.
