Study workflow
The product follows a fixed left-to-right flow. You can revisit earlier sections at any time, but downstream results may become stale if inputs change.
Data → Explore → Analyze → Interpret → History
Data — prepare inputs
Upload files, validate ingestion, map metadata, define experimental design, and save contrasts. Nothing in Analyze runs meaningfully until at least one dataset is ready.
Readiness signal: green dot on Datasets when a processed .h5ad exists.
Explore — first look
Inspect QC metrics, sample relationships, embeddings, and spatial layouts before committing to formal analysis. Explore is read-only with respect to the pipeline; it displays outputs from completed runs.
Analyze — compute
Run structured workflows: QC, normalization, clustering, differential expression, enrichment, spatial domains, biomarker discovery. Parameters are saved with every job. Failed runs show actionable errors on the Analyze and History pages.
Interpret — biological meaning
Connect numeric outputs to biology: cluster annotations, pathway enrichment, importable gene sets, disease evidence, and AI-assisted summaries grounded in computed results. Interpret aggregates results from multiple completed runs.
History — provenance
Review active and completed jobs, expand rows for parameters and errors, manage snapshots, and address stale outputs. Deleting runs is blocked when a snapshot references them or while a job is still running.
Typical single-cell path
| Step | Section | Action |
|---|---|---|
| 1 | Data | Upload .h5ad or convert 10x/CSV |
| 2 | Data | Save metadata and contrasts |
| 3 | Analyze | QC → Normalization → Clustering |
| 4 | Explore | Review UMAP and QC charts |
| 5 | Analyze | DE → Enrichment |
| 6 | Interpret | Review enrichment and gene sets |
| 7 | History | Review run records and create snapshot |
See section-specific guides: Data, Explore, Analyze, Interpret, History.