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

All our single-cell sequencing services provide you with: 

  • A preliminary data analysis;
  • A license for the BBrowser by BioTuring;
  • The option to start a custom data analysis project with us.

Preliminary data analysis for each project 

For all our single-cell sequencing services, a preliminary data analysis is included. 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 including the analysis. 

 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, a preliminary clustering analysis and differential gene expression analysis. 

 Use this preliminary analysis to analyze the cell populations present in your sample and their differential gene expression patterns. This will help you understand the results of your experiments right away. 

Example tSNE plot in our preliminary analysis

Analyze and visualize your data without coding

To further help you along, we provide all our clients with a free SCD license to the BBrowser from BioTuring.

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

Our license for the BBrowser allows you to:

  • Analyze subsets of cells, for example in clusters with large 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

Let us analyze your data

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

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

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

Our data scientists

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

What we can do

  • Basic processing of the data; including filtering based on QC, batch effect correction, normalization and dimensionality reduction
  • Clustering analysis and cluster characterization using differential gene expression analysis
  • Sample comparison using differential gene expression and gene set enrichment analysis
  • Trajectory inference and pseudotime analysis
  • Dataset integration with publicly available datasets or other data types
  • Sample demultiplexing using hashtag oligos


Our standard deliverables

For each single-cell sequencing project, you can expect the following deliverables:

  • FASTQ files
  • QC reports
  • Mapped count tables
  • A preliminary cluster analysis
  • A preliminary differential gene expression analysis
  • A Seurat object to do your own analyses with the Seurat pipeline

For 10x Genomics single-cell sequencing projects, we include some additional deliverables:

  • A cloupe object for easy visualization with the 10x Genomics Loupe Browser.


"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

Jan Willem Wijnands - Junior Data Manager

Jan Willem Wijnands

Data Manager

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