Welcome
Gradient BioSystems is a web-based workspace for transcriptomic analysis. Upload your data, run guided pipelines, explore results interactively, and assemble publication-ready figures — with full provenance for every step.
What you can do today
| Modality | Status |
|---|---|
| Single-cell RNA-seq | Full workflow: QC → normalization → clustering → DE → enrichment |
| Spatial transcriptomics | Domain clustering, spot viewer, gene overlays (Visium-class .h5ad) |
| Biomarker discovery | Feature selection, classifier cross-validation, ranked gene panels |
| Bulk RNA-seq | Analysis API available; guided UI coming soon |
How the product is organized
Every analysis lives inside a study (called an experiment in the database). From the dashboard you create or open a study, then work through six sections:
- Data — upload datasets, metadata, design, and contrasts
- Explore — QC charts, UMAP, spatial preview, gene inspection
- Analyze — run pipeline steps (clustering, DE, biomarker, spatial)
- Interpret — annotations, enrichment, gene sets, methods provenance
- Figures — multi-panel layouts and PDF export
- Runs — job history, snapshots, stale-output warnings
Who this is for
- Wet-lab biologists who need a guided path without writing R or Python
- Computational biologists who want parameter transparency and reproducibility
- Core facility analysts who run repeatable workflows for many labs
Next steps
- Use cases — scenario guides for single-cell, spatial, biomarker, and bulk RNA-seq workflows
- Quick start — run your first single-cell study in minutes
- Key concepts — studies, datasets, runs, and snapshots
- Study workflow — how the six sections fit together