Data Consulting as a service

Our bioinformaticians are here to help unlock actionable biological insights from your single-cell data. Our exploratory single-cell sequencing data analysis is included with all our services with the option to add more complex analysis performed by our skilled team. 

Bespoke data consultingMeet our data experts

Data analysis at Single Cell Discoveries

All our services include an exploratory data analysis

Bulk and single-cell RNA sequencing analysis can be complex, so we provide an exploratory data analysis with every project to give you a running start and ensure our experiments lead to actionable insights for your project. Hence, we forego standard pipelines, review all data output, and adjust parameters where needed before sending you your data. Right away, you can check the QC data, get a first idea of cell clusters, and study preliminary gene expression patterns.

View data report

Deliverables

Our standard deliverables to get you started

Every service includes a set of standard deliverables, ensuring that any scientist can quickly begin analyzing their data.

For single-cell sequencing data analysis, we deliver:

  • Raw sequencing data (FASTQ files)
  • Raw and filtered gene count tables
  • An interactive exploratory data analysis report including QC, clustering, and differential gene expression analysis
  • A Seurat object to do your own analysis with the Seurat pipeline
  • An explanation from our data team about data quality metrics
  • Additionally, for 10x Genomics: A cloupe file for easy visualization with the 10x Genomics Loupe Browser
  • Additionally, for VASA-seq: Spliced/unspliced count tables

For bulk RNA sequencing data analysis, we deliver:

  • Raw sequencing data (FASTQ files)
  • Gene count tables
  • An interactive exploratory data analysis report, including raw and mapped reads per sample and a PCA plot
  • Finally, an explanation from our data team about data quality metrics

For Discovery-seq data analysis, we deliver:

  • Raw sequencing data (FASTQ files)
  • Gene count tables
  • QC report of mapping results (UMIs per sample)
  • An explanation from our data team about data quality metrics

For Visium HD data analysis, we deliver:

  • Raw sequencing data (FASTQ files)
  • High-resolution microscopy images
  • CytAssist images
  • Feature barcode matrices in H5 format for 2, 8, and 16 µm bins
  • A cloupe file for easy visualization with the 10x Genomics Loupe Browser
  • An interactive exploratory data analysis report
  • An explanation from our data team about data quality metrics
  • A Seurat object to do your own analysis with the Seurat spatial workflows

All raw sequencing data, results, and reports are processed on EU servers, and securely encrypted using an AES (Advanced Encryption Standard) algorithm with a 256-bit key, before being delivered to the customers and archived.

Single Cell Discoveries workplace
Preview of our exploratory data report

View our exploratory data report

After each sequencing project, you will receive a data report with a comprehensive and easily accessible exploration of your data. Here, you can have a look at an example of our data report.

 

View data report

Bespoke data consulting

Our data scientists can maximize your biological discovery

Our data consultancy service is designed for scientists seeking easy access to deep bioinformatics expertise. Rely on us for fast, flexible analysis — whether it’s rapid, hassle-free interpretation of transcriptomic data, custom publication-ready figures, or guidance for future hypotheses. You bring the biological insight; we bring the analytical power.

It does not matter whether your transcriptome data was generated with us or somewhere else—we’re here to help uncover actionable insights. For all assays, we can:

  • Perform comprehensive quality control, normalization, and batch correction as needed
  • Curate data with expert, customized approaches
  • Apply dimensionality reduction techniques (e.g., PCA, UMAP, PHATE) and generate intuitive visualizations
  •  Cluster cells or samples using unsupervised learning methods
  • Conduct differential expression analysis across samples, clusters, or cell types
  • Perform gene set enrichment and pathway analysis
  • Produce high-resolution, publication-quality figures
  • Deliver tailored analyses based on your specific goals, following a detailed consultation
Bespoke data consulting

For single-cell sequencing data analysis, we can also help you with:

  • Cell type identification
  • Cell label transfer using annotated, publicly available datasets
  • Dataset integration, including with publicly available datasets
  • Sample demultiplexing using hashtag oligos or SNPS

For bulk RNA sequencing data analysis, we can also do:

  • Deconvolution of cell type abundances using single-cell reference datasets

For Discovery-seq analysis, we can also do:

  • Hit identification based on candidate target genes or pathways

For Visium HD we can also help you with:

  • Identification of spatially defined tissue domains
  • Generation of spatially aware clusters, within or across samples
  • Tissue domain annotation
  • Spot deconvolution using annotated scRNAseq reference datasets
  • Integration with single-cell datasets
Single Cell Discoveries lab
THE DATA SCIENCE TEAM

Meet our experts

Click on a profile to read more personal info.

HEAD OF DATA SCIENCE

Sofia Drobysheva, Junior Data Scientist at Single Cell Discoveries
DATA SCIENTIST

DATA SCIENTIST

Pablo Gómez Sacristán, Junior Data Scientist at Single Cell Discoveries
BIOINFORMATICIAN

DATA SCIENTIST

Tiago Figueiredo
BIOINFORMATICIAN

How can we help?

Want to supercharge your project with our bespoke data consulting?

Connect with our PhD-level scientists to discuss your project.