Data analysis

Bioinformatics 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. 

Custom data analysis Meet 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

You can rely on the standard deliverables included with every service. Consequently, we ensure that any scientist can get a head start with 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 object 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

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.

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

Custom Data Analysis

Our data scientists can maximize your biological discovery

We designed our data consultancy service for scientists who want easy access to extensive bioinformatics expertise. Leverage our capacity, time, and skill to gain additional analysis upon request. Get quick and effortless single-cell data, custom figures ready for publication, or directions for future hypotheses. Profit from our data analysis experience while we are guided by your biological expertise. 

It does not matter whether your transcriptome data was generated with us or somewhere else—we’re here to lend a hand in uncovering actionable insights.

Custom Data Analysis

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

  • Extensive QC and data curation + batch effect corrections
  • Clustering analysis to direct 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
  • Create plots of particular interest, publication-ready and high-resolution

For bulk RNA sequencing data analysis, we can do:

  • Data processing, curation, normalization, and QC
  • Sample comparison using differential expression
  • Gene set enrichment analysis
  • Deconvolution of cell type abundances using single-cell datasets

 

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Pere Català Quilis MERLN Institute for Technology-Inspired Regenerative Medicine

"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."

BioTuring BBrowserX

Analyze data without coding

Our partnership with BioTuring enables interactive single-cell data analysis without coding. This gives you the power to:

  • Analyze cell subsets—e.g., in clusters with high heterogeneity;
  • Find candidate marker genes and proteins;
  • Perform gene set enrichment analysis;
  • And more…
  • View our support page for more information and instructions.
THE DATA SCIENCE TEAM

Meet our experts

Click on a profile to read more personal info.

Andrei Prodan, Head of Data, Single Cell Discoveries
HEAD OF DATA

Nathalie Groen, Data Scientist, Single Cell Discoveries
TEAM LEAD DATA CONSULTING

Jan-Willem Wijnands, Data Manager, Single Cell Discoveries
DATA MANAGER

Jessie van Buggenum, Senior Data Scientist, Single Cell Discoveries
SENIOR DATA SCIENTIST

Empar Baltasar Perez, Junior Data Scientist at Single Cell Discoveries
JUNIOR DATA SCIENTIST

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

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

How can we help?

Want to supercharge your project with our custom data analysis?

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