cellpatri

Services & pricing

Three ways to work with us, depending on where your data is now. Prices are per sample unless stated; we confirm the exact cost before any work starts.

Standard analysis

From US$150

per sample

For data already through Cell Ranger. You upload the count matrix in the portal and the analysis runs straight away.

  • Quality control and filtering
  • Doublet detection and removal
  • Normalisation and variable genes
  • UMAP map and Leiden clustering
  • Marker genes for every cluster
  • Suggested cell type per cluster
  • Plain-language HTML report
  • Processed .h5ad and spreadsheets

Results usually within an hour of upload. You can re-run with different settings at no extra cost within 30 days.

Analysis from FASTQ

From US$300

per sample

For raw sequencing reads. We align them with Cell Ranger against the right reference genome, then run the standard analysis.

  • Everything in Standard analysis
  • Cell Ranger alignment and counting
  • Human, mouse or custom reference
  • Cell Ranger web summary for each sample

Usually 2–4 working days, depending on sequencing depth.

Custom analysis

Quoted per project

after a free 30-minute call

For questions that go beyond one sample. We agree the plan with you first, then work through it together.

  • Integrating several samples or batches
  • Comparing conditions (pseudobulk differential expression)
  • Reference-based cell type annotation
  • Subclustering a population of interest
  • Trajectory and pseudotime analysis
  • Publication-ready figures
  • A call to walk you through the results

Typically 1–3 weeks.

What you can upload

If you're not sure which files you have, send us a message and we'll tell you which one to upload.

FileWhere it comes fromAnalysed automatically?
filtered_feature_bc_matrix.h5Cell Ranger outs/ folderYes
filtered_feature_bc_matrix folder, zippedCell Ranger outs/ folder (matrix.mtx, barcodes, features)Yes
.h5ad with raw countsScanpy, CELLxGENE, or exported from another toolYes
FASTQ files (.fastq.gz)Your sequencing facilityNo: upload them and we align them for you
Seurat .rdsRNo: contact us and we'll convert it

Questions

I've never analysed single-cell data. Is this for me?

Yes, that's who we built it for. The report explains every figure in plain language, and the suggested cell types give you a starting point to check against what you know about your tissue.

How large can my files be?

The portal accepts files up to 500 GB. Uploads go in pieces straight to secure storage, so you can upload large FASTQ files from a normal browser.

Where is my data stored, and who can see it?

On Amazon Web Services in Sydney, Australia, encrypted at rest. Only your account can see your files. Each analysis runs on its own computer, which is deleted when the job finishes. Uploads and results are deleted automatically after 180 days.

Can I change the settings and run it again?

Yes. When you start an analysis you can change the quality thresholds and the clustering resolution. Higher resolution splits cells into more, smaller clusters.

Will the results work with Seurat?

The processed .h5ad file opens directly in Scanpy and CELLxGENE, and converts to Seurat with tools such as zellkonverter. The spreadsheets open in Excel.

Not sure which option fits?

Ask us