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Research Areas

Computational BiologySingle-cell, bulk RNA-seq, spatial, and biomarkers
CardiologyCardiovascular signals, cohorts, and interpretationImmunologyImmune cell states, signaling networks, and repertoire dynamicsNeurologyBrain connectivity, functional imaging, and electrophysiologyOncologyTumor microenvironment, immune response, mutations, and survivalPathologyWhole-slide imaging, tissue quantification, and spatial pathology

Application

Documentation

Documentation

Back to studies

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 obs columns
  • 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 or samples. Useful for confirming marker genes before interpretation.

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.