Observational single-cell data often blurs drivers and bystanders, especially when cell states collapse into broad labels. Nygen resolves state-level identity with structured evidence so teams can focus on biology that is more likely to matter.
Decode every cell
Nygen is the AI-native interpretation layer for single-cell omics, built to surface what traditional analysis leaves behind. Deeper signal, faster clarity, better decisions.
Powering discovery at the world's leading research institutions.
A focused product stack for single-cell programs.
We push single-cell programs past description into discovery. Our technology surfaces the biology that conventional workflows miss and translates it into insight you can trace, audit, and act on.
CyteType report walkthrough showing cell characterization of single-cell RNA-seq data with annotation evidence, confidence scores, and cell state summaries.
Explore product
Reasoning Engine
Flagship
CyteType
Structured AI reasoning that assigns cell identity the way a domain expert would. Confidence-scored, evidence-backed, fully auditable.
ScarfWeb collaborative analysis preview
Explore product
GUI Workbench
ScarfWeb
Distributed, secure infrastructure for intuitive secondary analysis, browser-native.
Where single-cell decisions shape outcomes.
Identifying druggable targets with genuine cell-type specificity requires analytical depth that standard workflows rarely deliver.
Most targets appear across multiple populations, so selectivity is easy to overstate. Nygen shows expression in precise cellular context, making target specificity easier to judge and defend.
Rare pathogenic states can disappear inside standard clustering and annotation workflows. Nygen helps surface low-frequency populations before they get averaged away.
Translating single-cell signatures into minimal, scalable clinical assays requires robust marker selection from underpowered cohorts.
Responder biology often lives in subtle cell states, but single-cell cohorts are usually too small to trust loose labels. Nygen gives biomarker teams reproducible state annotations they can carry into larger validation studies.
A strong single-cell signature still has to collapse into a practical assay. Nygen separates defining markers from passenger signal, making panel reduction more disciplined.
Site effects, handling differences, and compositional shifts can create biomarkers that fail on replication. Nygen applies the same annotation logic across batches so the signal stays more consistent.
Confirming that preclinical findings translate to human biology at the cellular level is the make-or-break step before clinical commitment.
Cross-species mapping breaks down when transcriptomes diverge, especially in immune and stromal compartments. Nygen anchors comparison in structured marker evidence, not similarity alone.
Organoids and iPSC systems rarely mirror full tissue complexity. Nygen helps teams compare model and primary tissue on the same cell-state frame so gaps are easier to spot.
A conserved gene does not guarantee a conserved regulatory context. Nygen captures the surrounding cell-state program so translation risk is clearer before clinical commitment.
Trial teams need stratification, mechanism-of-action clarity, and reproducible correlative biology from precious, limited biopsy material.
Trial biopsies are limited, variable, and impossible to repeat once lost. Nygen extracts consistent cell-state profiles from precious samples so baseline stratification starts from something reproducible.
Longitudinal samples are hard to compare when biology and technical drift move together. Nygen keeps annotation logic consistent across timepoints so resistance signals are easier to trust.
Single-cell findings only matter if they can support the broader trial story. Nygen produces traceable, versioned annotations that are easier to project, review, and defend.
Linking manufactured product attributes to clinical outcomes requires resolving functional cell states that standard phenotyping misses.
Every manufactured product starts from different patient material, so outcome links are noisy by default. Nygen resolves functional T cell states with the consistency needed to compare small cohorts.
Small protocol changes can reshape the final product in ways surface phenotyping misses. Nygen makes those shifts visible at cell-state resolution so manufacturing decisions are easier to interpret.
Post-infusion tracking is sparse, and infused cells are hard to separate from the host background. Nygen helps follow differentiation and exhaustion signatures so in vivo fate is clearer.
Identifying which cell types are damaged, at what dose, and whether the effect is on-target or off-target requires annotation that maps cleanly to pathology frameworks.
Sensitive tissues pick up dissociation stress quickly, making true compound effects hard to isolate. Nygen applies the same structured annotation across controls and treated groups to sharpen that comparison.
Safety teams need to know whether toxicity follows target biology or hits unrelated cell populations. Nygen provides the cell-type specificity needed to assess mechanism with more confidence.
The most useful safety signal often appears before histopathology changes become obvious. Nygen resolves early state shifts that can help bridge molecular findings to the pathologist's frame.
Our Technology
We build AI for single-cell biology from the ground up. Every layer of the stack, computation, annotation, interpretation, exists because we believe single-cell omics will solve problems that have stalled drug discovery for decades. That belief drives everything we build.
Purpose-built AI for single-cell biology. From computation to annotation to interpretation, every layer exists to advance drug discovery.
Our TechnologyRapid & scalable analysis
SOC 2 Compliant
Verified controls for security, availability, and confidentiality.
ISO 27001 Certified
Information security management system certification.
Data Retention
Zero data retention option available. Deletion within 1 hour, configurable per account.
Data Residency
Geographic region selection for data processing and storage.
LLM Provider Agreements
Data Processing Agreements and Zero Data Retention contracts with OpenAI and Anthropic.
Data Transmission
Only pseudo-bulk expression data transmitted to servers. Local SDK option available.
Access Control
Password-protected reports, role-based access within your organization.
Instant Analysis
Scalable cloud infrastructure across 22 AWS regions. No queues, no pipeline bottlenecks.
Latest from Nygen
Your data has more to say.
Talk to our team about how Nygen can fit into your single-cell discovery workflow.