Data Analysis

The analysis of single-cell sequencing data is complex and can seem daunting. But we are here to help you out.

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Single-cell data analysis


Since single-cell sequencing analysis can be complex, we have multiple solutions included with our services. 

All our single-cell sequencing services provide you with the following: 

Preliminary data analysis

Preliminary data analysis is included with all our single-cell sequencing services. In contrast to popular preliminary analyses with standard pipelines, we review our data output and adjust parameters where necessary before we send you the data.  Next to the raw data files, we present this preliminary data accessibly in our data reports.

The preliminary data analysis is an analysis we do ourselves to check the quality of your data and to give you a first idea of your results.

Besides the raw sequencing data (FASTQ format), we send you quality control reports, mapped count tables, preliminary clustering, and differential gene expression analyses. 

You can use this preliminary analysis to analyze the cell populations present in your sample and their differential gene expression patterns. This will help you get an understanding of your results right away. 


2D t-SNE plot from single-cell data that shows seven clusters of cells

Example tSNE plot in our preliminary analysis


Analyze without coding

To further help you, we provide all our clients with an SCD license to the BBrowserX from BioTuring.

Our partnership with BioTuring allows you to analyze all your single-cell sequencing data without code interactively!

Our license for the BBrowserX allows you to:

  • Analyze subsets of cells, for example, in clusters with significant heterogeneity
  • Find marker genes and proteins
  • Perform enrichment analysis
  • And much more!

Combine BioTuring with our preliminary data analysis to quickly understand and analyze your results, create publication-ready graphs, and draw conclusions within hours.

For more information and instructions, view our support page, or watch our webinar with BioTuring for a demo!

Example of single-cell data in the BBrowser.

Custom data analysis

Don’t have the time or in-house expertise to analyze your results? Struggling with a complex research question?

We provide additional or complete analysis upon request. Our team of bioinformaticians is highly skilled and experienced with bulk RNA sequencing and single-cell data.

If your data was generated with us, email to arrange your data analysis project.

Our data scientists

Nathalie Groen
Janneke Hulsen - Data Scientist
Janneke Hulsen
Empar Baltasar Pérez

"For me, the collaboration with the data analysis service was fantastic. Nathalie had the expertise in terms of data analysis, and I have more biological expertise. So whenever I asked a question, she would propose a solution. Or then, when she was asking a question, I would propose some solution. It was excellent work in tandem."

Pere Català Quilis, PhD candidate
MERLN Institute for Technology-Inspired Regenerative Medicine

Below is an overview of our standard and optional deliverables.

Single-Cell RNA Sequencing

Our standard deliverables:
  • Raw sequencing data (FASTQ files);
  • Raw and filtered gene count tables;
  • A preliminary analysis report (including QC, clustering, and differential gene expression analysis);
  • A Seurat object to do your own analysis with the Seurat pipeline,
  • [For 10x Genomics:] A cloupe object for easy visualization with the 10x Genomics Loupe Browser
What we can do in a custom project:
  • Extensive QC, data curation, and batch effect correction;
  • Clustering analysis to guide cell type identification;
  • Cell label transfer using annotated, publicly available datasets;
  • Sample comparison using differential expression and gene set enrichment analysis;
  • Dataset integration with (publicly available) datasets;
  • Sample demultiplexing using hashtag oligos or SNPs;
  • Generate plots of interest, publication-ready and high-resolution.

Bulk RNA Sequencing

Our standard deliverables:
  • Raw sequencing data (FASTQ files);
  • Gene count tables;
  • QC report of mapping results (raw and mapped reads per sample, PCA plot).
What we can do in a custom project:
  • Data processing, curation, normalization and extensive QC;
  • Sample comparison using differential expression;
  • Gene set enrichment analysis.
Jan Willem Wijnands - Data Manager

Jan Willem Wijnands

Data Manager

Questions about your data or in need of custom analysis?
Contact us for advice.