scellrunv1.3.3

A contract research organization receives dozens of cellranger outputs per month from pharma clients and needs reproducible, report-first analyses without bespoke scanpy scripts per project. An agent runs scellrun convert + analyze on each dataset and delivers the generated HTML/PDF reports with plain-language summaries to non-computational clients. The version compatibility check ensures every run is defensible under the same validated toolchain.

A university genomics core supports bench scientists who generate 10x mtx and h5ad files but cannot write Python. An agent SSHes into the core's HPC, sets up the environment, and runs scellrun analyze end-to-end, then translates decision logs and cluster annotations back to the scientist. The review Flask UI lets the scientist override cluster labels interactively from their browser.

A translational medicine team analyzes patient tumor biopsies to characterize immune infiltration and tumor heterogeneity. The agent uses scellrun's tumor cross-disease profile with celltype_broad panels to produce standardized reports across a cohort, then exports PDFs for tumor board and regulatory documentation. Any cluster-label disagreements are resolved via the review UI and reapplied with --apply-overrides.

A neuroscience lab compares single-cell profiles from cortical organoids against published brain datasets. The agent leverages the brain cross-disease profile for initial broad celltype calls, regenerates reports as new samples arrive with scellrun report, and flags where fine-subtype taxonomies are unavailable so the scientist knows the limits. Results feed into grant progress reports and preprints.

A hospital-affiliated lab processes kidney biopsy scRNA-seq to identify cell states associated with fibrosis progression. An agent runs scellrun analyze with the kidney profile, applies reviewer overrides for ambiguous tubular cell clusters, and exports print-ready PDFs for the clinical research team. Decision provenance (source=user vs pipeline) is preserved for audit.

A bioinformatics consultancy offers monthly retainers where clients submit h5ad or cellranger outputs and receive annotated reports, PDF exports, and plain-language interpretations within days. The agent automates the scellrun pipeline, review-UI handoffs, and report generation while a human scientist validates final interpretations. Pricing tiers scale by sample volume and turnaround time.

A university or hospital core facility licenses an agent-orchestrated scellrun workflow to serve internal labs, with governance around version pinning, override audit logs, and reproducible artifacts. Revenue comes from annual site licenses plus user-seat fees, with premium support for version upgrades and custom profile validation. Facilities avoid hiring additional bioinformaticians per project.

A biotech partners with pharma R&D teams to deliver standardized cross-disease scRNA-seq profiling (tumor, brain, kidney) under a collaborative data-sharing agreement. The agent runs scellrun at scale across cohorts, and revenue is structured as milestone payments tied to biomarker discoveries plus per-cohort analysis fees. Cold-validation runs for new profiles are sold as add-on engagements.