Genomics & transcriptomics
Single-Cell RNA-seq Analysis
We analyse single-cell RNA-seq datasets from count matrices to annotated cell populations and between-condition comparisons, with every filtering and clustering choice documented and figures ready for a manuscript.
Who it is for
- Labs with 10x Genomics or similar droplet data
- Projects comparing conditions or time points across samples
What you send us
- Cell Ranger outputFiltered or raw matrix, features and barcodes.
- h5ad or Seurat objectsExisting analyses to extend or review.
- Sample metadataDonor, condition, batch and chemistry.
What you receive
- Annotated object (h5ad or RDS)
- Cluster markers and annotation evidence
- UMAP, dot-plot and composition figures
- Pseudobulk differential-expression tables
- Methods and notebooks
Methodology
How the work runs
Each step is agreed with you and documented. Typical tools: Scanpy · Seurat · scrublet · Harmony · scVI · CellTypist · DESeq2 (pseudobulk)
- ScopingSamples, conditions, expected cell types and the comparisons that matter.
- QC and filteringCell and gene filtering, doublet and ambient-RNA handling, with thresholds documented per sample.
- Integration and clusteringNormalisation, integration across samples and graph-based clustering at a justified resolution.
- AnnotationMarker- and reference-based cell-type annotation, reviewed with you before it is final.
- Comparison and reportCell-type composition and pseudobulk differential expression between conditions.
Quality controls
Checks applied to every project
- Per-sample QC distributions and thresholds reported
- Doublet rate estimated against the expected rate for the loading
- Integration checked for over-correction of biological differences
- Cluster stability across resolutions and random seeds
Scope and limits
What the work can and cannot show
- Between-condition comparisons need biological replicates (donors or animals), not only many cells.
- Research use only: results are not a clinical or diagnostic report.
Free quote
Start a Single-Cell project.
Describe your data and questions. We reply with questions or a written quote.
It depends on the data type, the number of samples and the depth of interpretation you need. Every project receives a written quote with scope, deliverables, price and delivery date after a short exchange about your data and questions. The quote is free and carries no obligation.
Data are used only for your project, transferred through a channel you approve and deleted at the end of the engagement on request. We will sign your institution’s confidentiality agreement before any data are shared.
Yes. You receive a methods section with software versions and parameters, and every figure can be regenerated from the delivered code. Authorship or acknowledgement follows your field’s norms and is agreed at the start.
Related