FAQ

Why does the URL say "experiment" but the UI says "study"?

They are the same object. Study is the user-facing label; experiment is an older internal name that still shows up in some URLs.

I uploaded a file but analysis fails with "dataset not found"

Confirm ingestion status on Data → Datasets is ready, not failed. For CSV or 10x uploads, run Convert and wait for completion before starting Analyze.

Enrichment returns no terms

Check that your gene symbols match the reference database (HGNC for human demo data). Synthetic names like GENE001 will not match GO annotations. Re-run DE after fixing gene names in var.

Why are my results marked stale?

Changing metadata, design, contrasts, or re-running an upstream step (QC, normalization) invalidates downstream results. Open History → Stale outputs and re-run the listed steps.

Can I delete a pipeline run?

Yes, from History, unless the run is still active or referenced by a snapshot. Delete the snapshot first if needed.

Does the platform run R or Seurat?

No. Algorithms are Python ports inspired by Seurat, Bioconductor, and KnowSeq.

Where is bulk RNA-seq in the UI?

Bulk RNA-seq is available in Analyze → Bulk RNA-seq. The guided step lets you set the condition column, optional reference/test levels, filtering, normalization, VST, LFC threshold, and FDR cutoff, and the results view includes sample QC, PCA/sample-distance diagnostics, and mean-variance tables. Set operations and standalone report generation are still expanding.

Is AI interpretation available?

Yes. Interpret → AI Summaries and the Analyze buttons on the UMAP cluster panel, DE results page, and enrichment results page request grounded narrative summaries (cluster annotation, DE interpretation, enrichment interpretation, and study summary with draft methods text). The model reads structured run results only — it does not compute p-values, fold changes, or any other statistic; every cited metric must already exist in the run's result payload. Disease Evidence remains a separate, non-AI curated gene-association lookup.

Where did the Figures page go?

Study-scoped figure building moved into a cross-area report composer at /report, which assembles panels from completed runs across studies into an exportable PDF. Old /experiments/{id}/figures links redirect there automatically.

How do I get help or report a bug?

This product is under active development. Contact your workspace administrator for support.