Your single-cell data,
ready to explore

ScarfWeb is the browser-based analysis layer for single-cell omics. Explore clusters, run marker analysis, annotate cell types, and share reproducible findings — without writing code or provisioning compute.

Interactive analysis at research scale

1,500+ researchers analyzing
100+ top global institutions
ISO 27001 + SOC 2 certified

Upload your own data or connect to curated datasets and start working immediately. ScarfWeb handles the infrastructure so your team can focus on the biology. Publication-ready outputs, reproducible workflows, and real-time collaboration are built in.

Walk through a complete analysis

From data upload to annotated clusters and shareable figures.

Built for the way researchers actually work

No-code, full-stack analysis

No-code, full-stack analysis

Every step from QC to differential expression runs through a visual interface with adjustable parameters. Researchers drive their own analysis without writing code or waiting on bioinformatics queues. The same workflows are fully reproducible, versioned, and auditable.

AI-powered cell characterization

AI-powered cell characterization

CyteType runs directly inside your analysis session. Automated cell annotation with confidence scoring, marker-level evidence, ontology mapping, and literature linking. Review and override at the cluster level. No separate tool, no export required.

One workspace, every collaborator

One workspace, every collaborator

Bench scientists and bioinformaticians work in the same dataset, the same session. Share results via public links or private access, publish to Nygen Database, or export for scripted pipelines. The analysis stays in one place regardless of who needs to see it.

What ScarfWeb does

Every step of single-cell analysis — data management, processing, visualization, statistical testing, and collaboration — in one browser-based workspace.

Get your data in. Keep it organized.

Flexible matrix upload

Upload preprocessed count matrices in common formats including MTX, H5AD, H5, and CSV. Drag, drop, analyze.

R P

CITE-Seq and multi-modal ingest

Upload transcriptomic and protein-level data together. ADT and HTO data are detected and separated automatically during import.

Merge and demultiplex

Combine datasets across samples, batches, or conditions. Demultiplex HTO-labeled pools without external tools.

Metadata and external analysis import

Bring in sample annotations, condition labels, or existing clustering results from Seurat, Scanpy, or other pipelines. No reformatting required.

Bulk metadata editor

Update cell-level and sample-level annotations across your dataset in one step.

Designed for discovery, built for trust

Every layer of ScarfWeb is built to keep your data secure, your analysis reproducible, and your outputs defensible.

No install, no queues

Runs entirely in the browser on scalable cloud infrastructure across 22 AWS regions. Upload your data and start working — no local compute, no pipeline setup.

Publication-grade output

Peer-reviewable figures, exportable tables, and auto-generated methods sections. Every output traces back to the exact parameters used.

Secure by default

ISO 27001 certified, SOC 2 compliant, fully GDPR adherent. Data encrypted at rest and in transit with comprehensive backups.

Reproducible by design

Full version control across every analysis session. Every parameter, filter, and selection logged and shareable.

Trusted by researchers from

Mass General Brigham
Memorial Sloan Kettering Cancer Center
Harvard University
University of Oxford
University of Cambridge
Helmholtz Munich

See what your data can show you.

Start analyzing in the browser today, or talk to our team about how ScarfWeb fits your workflow.