ScarfWeb plans & licensing

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Built for single-cell researchers. Every paid plan unlocks the complete analysis toolkit; tiers change the scale you can run, how your team collaborates, and the licensing and support model. Academic pricing is set well below the cost of the sequencing it supports.

For universities, institutes, and core facilities running non-commercial research.

Free

For pilots and teaching

$0

Free forever

Up to 250k cells · 10 datasets

Get started
  • Full scRNA-seq, CITE-seq, and hashtag-multiplexed analysis
  • Merge and subset datasets
  • Import datasets from Nygen Database
  • Public shareable dataset links
  • In-app support and onboarding

Researcher

For PhD students, postdocs, and PIs

$99 /mo

Billed annually, or $149 monthly

Up to 1M cells · 40 datasets

Subscribe

Everything in Free, plus:

  • Advanced plots and customization
  • Advanced analysis tools, no rate limits
  • Unlimited analysis versions
  • Automated annotation with literature evidence
Most popular

Lab

When a lab collaborates

$249 /mo

Billed annually, or $399 monthly

Up to 5M cells · 200 datasets

Subscribe

Everything in Researcher, plus:

  • 5+ seats (1 PI seat), add members as needed
  • Private sharing and transfer within the lab
  • Consolidated billing
  • User management interface (coming soon)

Institution

For departments and institutes

Custom

Tailored to your needs

Custom scale and seats

Contact us

Everything in Lab, plus:

  • Dedicated bioinformatician for ongoing support
  • Onboarding seminars and webinars
  • Usage data and metrics

Annual billing saves about 33% versus monthly. Invoicing and purchase orders are available on Lab, Institution, and Enterprise plans.

Every plan includes the full single-cell toolkit

The complete analysis stack is available on every plan, including Free. Tiers change scale, seats, and licensing, not the science.

Preprocessing and embedding

  • Cell QC and filtering
  • Highly variable gene selection
  • Batch correction
  • PCA, k-NN graph, UMAP and t-SNE

Clustering and differential expression

  • Leiden and Paris clustering
  • Marker gene search
  • Custom differential expression
  • Pseudobulk aggregation

Functional and trajectory analysis

  • GSEA and gene-signature scoring
  • Compositional analysis
  • Pseudotime and trajectory inference
  • Imputation

Automated cell annotation

  • Confidence-scored cell-type labels
  • Cell Ontology linking
  • Literature-backed evidence trail
  • Anomaly detection and cross-dataset labeling

Modalities and data management

  • scRNA-seq (droplet and plate), CITE-seq, TCR/BCR (VDJ), spatial (Visium)
  • HTO demultiplexing, merge and subset
  • Dataset versioning and raw matrix download
  • Figure export to PNG, SVG, and CSV

Sharing and collaboration

  • Public links for datasets
  • Private sharing within a lab or team
  • Dataset transfer between members
  • Import from and label against Nygen Database

On the Free plan, advanced interactive analyses (differential expression, GSEA, gene signatures, trajectory inference, marker search, and Database label import) carry daily usage limits. Paid plans remove those limits.

Security and compliance on every plan

FAQs

Yes. It is free forever, with usage quotas and daily limits on advanced interactive analyses. No credit card is required.
ScarfWeb academic pricing is set well below the cost of generating the data it analyzes and typically replaces multiples of that in bioinformatics time. Email sales@nygen.io for institution-specific pricing.
Both are available. Annual billing saves about 33% versus paying monthly. You can change your cycle at renewal.
Yes, on Lab, Institution, and Enterprise plans. This suits institutional procurement and expense tracking. Contact sales@nygen.io to arrange it.
Datasets are counted in increments of 25,000 cells. A 70,000-cell dataset, for example, counts as three datasets toward your quota.
You receive notifications as you approach the limit. If you need more, contact sales@nygen.io and we will find the most cost-effective option.
Seats share a data quota across members, with one PI or admin seat included and the flexibility to add more. Admins manage access and resource allocation.
Data is hosted on AWS with multiple regions for residency, encrypted in transit and at rest, backed up daily, and run on ISO 27001 and SOC 2 aligned infrastructure. See the trust center at trust.nygen.io.
Datasets you have published stay accessible under their Creative Commons license. For private data, contact support@nygen.io about export and deletion.

Planning a license for your lab or institute?

Tell us your team size, expected data volume, and modalities, and we will put together pricing and a short walkthrough for your group.

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