Nygen Analytics

What Nygen Analytics does

Nygen Analytics AB is a Sweden-based private company (Aktiebolag) founded in 2022 and headquartered at Medicon Village in Lund, Sweden. It builds AI-driven cloud software for single-cell omics interpretation, serving two primary customer segments: biopharma R&D and translational teams (drug discovery, biomarker, cell therapy, toxicology, clinical trial) and academic research institutions. The homepage customer roster features more than ten universities, including Harvard, Oxford, Stanford, Cambridge, Helmholtz Munich, Memorial Sloan Kettering, and Institut Pasteur, alongside a single publicly disclosed commercial/biotech partner in U.S.-based VLP Therapeutics.

The product stack centres on CyteType, a deterministic AI workflow (rebuilt in January 2026 from a prior multi-agent system) that orchestrates six specialised agents — Contextualizer, Annotator, Reviewer, Summarizer, Clinician, and Chat — to assign cell identity anchored to Cell Ontology (CL) terms with confidence scoring, heterogeneity flags, and PubMed-linked evidence trails. It is delivered as open-source Python (pip install cytetype) and R (CyteTypeR) clients, a self-serve web dashboard, a Claude Model Context Protocol server exposing 23 tools, and commercial tiers. ScarfWeb is a browser-native secondary-analysis workbench running across 22 AWS regions, supporting batch correction (Harmony), pseudotime, HTO demultiplexing, and on-demand integrity checks. Adjacent products include Nygen Database (curated, GDPR-compliant multi-omics repository) and Nygen Insights (AI-driven auto-annotation inside ScarfWeb). Internal benchmarking reports 388%/268%/101% improvements over GPTCellType/CellTypist/SingleR on CyteOnto similarity across 977 clusters in 20 datasets, and the company holds a patent-pending portfolio on the underlying algorithms.

Nygen monetises CyteType and ScarfWeb via a hybrid subscription plus per-cluster usage model with three commercial tiers (Discovery, Enterprise, Partnership) offering private cloud, AWS Bedrock, and on-premises/air-gapped deployment with customer-managed LLMs. An open-source academic tier under CC BY-NC-SA 4.0 — capped at three annotation runs per day — functions as the top-of-funnel adoption channel. Distribution combines a self-serve product-led growth motion (PyPI/GitHub/Dashboard) with a CEO-led enterprise direct-sales motion (Calendly demo) supported by a heavy content and conference presence. The company holds ISO 27001 certification and SOC 2 attestation (June 2025), GDPR/CCPA compliance, zero-data-retention contracts with OpenAI and Anthropic, and a public Trust Center at trust.nygen.io. Headcount is 1–10 employees; disclosed funding consists of a $733,591 round from SmiLe Inject Capital (August 2024) and a 1M SEK Vinnova grant (November 2025).

Name

Nygen Analytics

Legal name

Nygen Analytics AB

Website

https://nygen.io

Company type

Private

Founded year

2022

Operating status

Operating

Headcount range

1–10 employees

Short description

Nygen Analytics provides an AI-native single-cell omics interpretation platform, anchored by its CyteType cell-type annotation engine and ScarfWeb browser workbench, serving biopharma R&D teams and academic research institutions across the US and Europe.

Ownership category

akta.pro rank

Product category

Bioinformatics Software

NAICS

Computer Systems Design and Related Services (54151), Software Publishers (5132)

SIC

Services-Computer Integrated Systems Design (7373), Services-Prepackaged Software (7372)

akta.pro primary industry

Bioinformatics & Multi-omics Analysis Software (HLAGAJAD)

akta.pro secondary industry

Model Serving, Inference & Deployment Platforms (APIs, Edge/On-Prem) (HDAEANAC)

Keywords

• Single-cell analysis
• Cell type annotation
• Bioinformatics software
• Omics data platform
• AI drug discovery

Headquarters

HQ city

Lund

HQ country

Sweden

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Technology or R&D, Personnel, Infrastructure, Marketing or Sales, Operations

Revenue model

1. Free Academic / Non-Commercial License: Open-source CyteType Python and R clients under CC BY-NC-SA 4.0; free personal tier with three annotation runs per day, plus organization-workspace licensing for academic collaborators. Zero direct revenue but acts as a top-of-funnel adoption and brand-building channel.
2. Commercial CyteType Subscription (Discovery, Enterprise, Partnership tiers): Annual subscription fee combined with per-cluster annotation usage-based cost; tiered across Discovery, Enterprise, and Partnership levels with options for private cloud, AWS Bedrock integration, and on-premises air-gapped deployments with customer-managed LLMs.
3. Per-Cluster Annotation Usage: Consumption component layered on top of the commercial subscription; customers can also bypass quotas by supplying their own LLM API keys, which shifts provider cost to the customer and acts as a hybrid usage pricing lever.
4. ScarfWeb Platform Subscriptions & Storage: Cloud-native single-cell analysis platform with subscription plans; data storage on AWS is included at no extra charge, while advanced features (e.g., on-demand integrity checks) are gated to certain subscription plans. Enterprise customers can negotiate SLAs.
5. Custom Analysis & Data Procurement Services: Professional services including data procurement from GEO/public portals (typically within one week), custom analysis support (modality integration, statistical significance, pathway enrichment, doublet detection, ADT normalization, multi-species sample merging, bulk figure generation), and upload support for non-standard file formats; Enterprise tier can negotiate SLAs.
6. Grant-Funded Collaborative Research: Non-dilutive grant funding (e.g., 1M SEK Vinnova 'Deepened collaboration with USA, UK and Singapore within Health and Life Science' grant with VLP Therapeutics) supporting joint development of predictive cancer-immunotherapy models and generating reference customer case studies.

Pricing tiers

Go-to-market motion5 records

Distribution channels1 record

Marketing channels10 records

Core offering

Nygen Analytics provides an AI-native interpretation layer for single-cell omics data, anchored by its CyteType reasoning engine that performs automated cell-type annotation using a multi-agent/deterministic AI workflow mapped to the Cell Ontology, and its ScarfWeb browser-native cloud workbench for distributed secondary analysis of single-cell RNA-seq data. Offerings are delivered as open-source Python and R clients, a hosted web dashboard, and a Claude MCP connector, with enterprise deployment options spanning private cloud, on-premises, and air-gapped installations.

Product overview

Nygen Analytics offers a platform-plus-modules architecture for AI-powered single-cell omics analysis, centred on four named products that together cover the full discovery workflow. CyteType is the flagship AI reasoning engine that assigns cell identity with structured, evidence-backed, auditable output; it is offered as a Python client, an R client (CyteTypeR), a web dashboard, a Claude MCP connector, and open-source code. ScarfWeb is the browser-native GUI workbench for distributed secondary analysis, embedding Nygen Insights for auto-annotation and connecting to the Nygen Database for publishing and discovery. The four products — CyteType, ScarfWeb, Nygen Database, and Nygen Insights — combine scalable cloud computation across 22 AWS regions, ISO 27001 and SOC 2 certified infrastructure, and AI-driven interpretation for biopharma and academic research teams.

Differentiator

Problem solved

Functional benefit

Brands

• CyteType: AI reasoning engine for single-cell omics cell-type annotation. Structured AI reasoning that assigns cell identity with confidence scoring, evidence-backed and auditable annotations.
• ScarfWeb
• Nygen Database
• Nygen Insights

Products and services

• CyteType Flagship AI reasoning engine for single-cell RNA-seq cluster annotation. Uses a six-agent (Contextualizer, Annotator, Reviewer, Summarizer, Clinician, Chat) deterministic AI workflow to assign cell identity with Cell Ontology (CL) term mapping, confidence scoring, heterogeneity flags, multi-expert synthesis, ranked pathway signals, and a linked PubMed citation trail. Available as Python and R clients, a web dashboard, and a Claude MCP server.
• ScarfWeb Browser-native, distributed cloud workbench for intuitive secondary analysis of single-cell data. Provides upload, QC, HVG selection, batch correction (Harmony), clustering, UMAP visualization, differential gene expression, compositional analysis, pseudotime, gene sets, and auto-annotation via Nygen Insights. Runs across 22 AWS regions with no queue bottlenecks.
• Nygen Database Curated, GDPR-compliant repository of harmonized single-cell multi-omics datasets for reuse and de-risking of early-stage discovery pipelines. Dataset publishing is integrated with the ScarfWeb workbench.
• CyteType Claude MCP Connector Model Context Protocol server that exposes 23 tools grouped into Session Management, Dataset Exploration, Annotation Introspection, and Annotation Deep Dive categories. Enables natural-language interaction with single-cell analysis results directly through Claude.
• AI-Driven Predictive Models for Cancer Immunotherapy (VLP Therapeutics collaboration) Joint analytical product offering with VLP Therapeutics to develop AI-driven predictive models that forecast which viral payloads will effectively activate anti-tumor immunity in specific patients from single-cell RNA-seq profiles.

Quantifiable outcome

• 388.52% higher CyteOnto similarity score vs. GPTCellType (identical GPT-5 model), 267.9% vs. CellTypist, 100.67% vs. SingleR (z = 8.04, 8.15, 8.36; p < .001) across 205 clusters in 4 datasets
• +5 more outcomes

Named customers17 records

Segments4 records

Ideal customer profiles4 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration11 records

AI capability10 records

Feature9 records

Partnerships

Five partnerships are on record, tiered flagship and core.

• VLP Therapeutics, Inc.flagshipStrategic or Co-development Partner · 11 November 2025Vinnova-funded 12-month co-development project (1M SEK / ~$105,000 grant) to build AI-driven predictive models for cancer immunotherapy. Builds on a prior collaboration that produced a joint bioRxiv preprint (Ishikawa et al., August 2025) and supports VLP's Phase 1 clinical trial at Stanford Medicine (NCT06736379, initiated August 2025) using its virus replicon particle (VRP) technology.
• Amazon Web Services (AWS)flagshipTechnology or IntegrationPrimary cloud infrastructure and storage provider, with Nygen's infrastructure spanning 22 AWS regions for instant analysis and no pipeline bottlenecks; AWS is ISO/IEC 27018:2019 certified and stores all user-provided data. Used for S3-based object storage with hardware fault tolerance, hourly/weekly backup routines, and SHA256 integrity verification.
• OpenAIcoreTechnology or IntegrationLLM provider with a Data Processing Agreement and Zero Data Retention contract; used for CyteType annotation across multiple agent roles, and one of nine supported providers in the bring-your-own-key configuration. Also available for direct API key configuration in the Python and R clients.
• AnthropicflagshipTechnology or IntegrationStrategic LLM provider with a Data Processing Agreement and Zero Data Retention contract; powers the CyteType annotation agent roles, and supported as both default and configurable backend (including AWS Bedrock-hosted claude-3-5-sonnet). Featured in the CyteType MCP connector integration with Claude.
• Stanford MedicinecoreImplementation/ SI/ Consulting PartnerSite of the Phase 1 clinical trial (NCT06736379) initiated by VLP Therapeutics in August 2025, in which Nygen's predictive single-cell models are used to analyse immunotherapy response. Stanford University is also featured on the homepage as a research-institution user.

Scale indicators11 records

Recent moves6 records

Expansion highlights7 records

Market position

Strengths5 records

Weaknesses4 records

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

• GitHubgithub.com/NygenAnalytics/CyteType
• LinkedInlinkedin.com/company/nygen

Compliance5 records

Revenue estimate

Valuation estimate

Number of profiles

Profiles2 records

Funding overview

Funding rounds2 records

Investors2 records

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Nygen Analytics