Single-cell sequencing 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 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 email@example.com to arrange a data analysis project.
Our data scientists
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.