Explore
Explore is where you inspect study quality and preview structure before and after formal analysis.
Overview
The overview panel summarizes dataset metrics, completed runs, and a checklist of available views (embedding, spatial, QC).
Embedding (UMAP)
Opens the WebGL UMAP explorer for the latest completed clustering run. You can:
- Color points by cluster, sample, condition, or other
obscolumns - Select clusters and inspect marker genes
- Navigate to DE results for a selected cluster
Requires a completed Clustering run.
Spatial
Opens the spatial viewer when the dataset has spatial coordinates and a completed Spatial domains run. Overlay gene expression on tissue coordinates and inspect domain assignments.
Sample QC
Displays histograms, retention rates, and per-sample breakdowns from the latest QC run. Use this to decide whether filter thresholds in Analyze need adjustment.
Genes
Inspect individual gene expression across cells, samples, or spatial spots. The Genes panel keeps one selected gene linked across the searchable gene list, expression metrics, UMAP expression panel, cluster/sample/domain summaries, result-page links, and a browser-saved working gene list.
Use Export on linked summary panels to download the current selected-gene summaries as CSV.
What Explore does not do
Explore does not start pipeline jobs. To change QC thresholds or re-cluster, go to Analyze. Re-running upstream steps marks downstream results as stale.