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 (genes, UMIs, % mitochondrial, % ribosomal, % hemoglobin), retention rates, and per-sample breakdowns from the latest QC run, plus the Stress and cell-death signatures table: for each signature, the genes found, median % counts and module score, and per-sample (or per-condition) medians. Click a signature for its gene list and source. Below it, the Assay type note, the Doublets panel (per-sample expected and observed doublet rates, thresholds, and score distributions), and, when the ambient step has run, the Ambient RNA panel (contamination fraction, counts removed per cell, the most abundant soup genes). Use this to decide whether filter thresholds in Analyze need adjustment and whether a sample shows handling artefacts. See Single-cell analysis.
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.
Click View 3D structure to see the selected gene's protein on its AlphaFold model, coloured by model confidence, with curated domains you can click to focus. The protein is resolved for the study's organism (human, mouse, or rat) from bundled UniProtKB tables on the server, so no third-party request is made from your browser. The card stays collapsed until opened. Below the model, Experimental complex with finds the best-resolution PDB entry containing the gene's protein and a partner you name (for example CDK8 with CCNC) and highlights the interface residues on each side.
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.