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.
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.
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.
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.
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
"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
Andrei Prodan, PhD, is responsible for coordinating the SCD Data Science team, updating and maintaining computational infrastructure, and managing research collaborations. Before SCD, he worked as Senior Data Scientist at NIZO, a Dutch CRO doing research for the Food and Pharma industries. Prior, he was a postdoctoral researcher in Bioinformatics at the AMC Amsterdam for 4 years analyzing human clinical trial and cohort data, and obtained his PhD at the Free University Amsterdam. He enjoys running, hiking and reading.
HEAD OF DATA
Nathalie Groen
TEAM LEAD DATA CONSULTING
Nathalie Groen, PhD, helps our customers get the most out of their data as team lead of the data analysis project scientists. Next to that, she is a PostDoc at the Hubrecht Institute, where she works on building a cell atlas on the human pancreas. She obtained her PhD in computational biology at the University of Twente. She first started working with single-cell data as a PostDoc when studying β-cell biology in the context of diabetes. At home, she is using Raspberry Pi's to smarten things up.
TEAM LEAD DATA CONSULTING
Jan Willem Wijnands
DATA MANAGER
Jan Willem's main focus is on maintaining the data analysis pipeline at Single Cell Discoveries. He completed his BSc degree in Bioinformatics at the University of Applied Sciences Leiden and his MSc degree in Evolutionary Biology at Leiden University. During his research internships, he mainly worked on the phylogenetics of bacteria, orchids, and banded newts at Institute Biology Leiden and Naturalis Biodiversity Center. Out of office hours, his inner nerd gets triggered by all types of gadgets to establish a smarter home.
DATA MANAGER
Jessie van Buggenum
SENIOR DATA SCIENTIST
Jessie van Buggenum, PhD, is senior data scientist responsible for custom data analysis projects for our clients. She has obtained the VENI research grant and was key computational investigator for two public-private partnerships in single-cell multiomics prior to starting at Single Cell Discoveries. Her PhD she obtained in molecular developmental biology, where she developed sequencing methods ID-seq and RAID.
Her love for photography earned her the Gup News talent award in 2021 for a documentary on her grandfather. In addition, she loves gravel biking, backpacking and camping in Scandinavia.
SENIOR DATA SCIENTIST
Janneke Hulsen
DATA SCIENTIST
Janneke analyzes and interprets single-cell sequencing data to uncover useful insights. She studied Philosophy and Biomedical Sciences, specializing in immunology with a Master's degree in Infection & Immunity. Next to performing data analyses at SCD, she pursues a second master’s in Bioinformatics to further expand her programming skills. Her inner nerd is excited to learn programs and languages: from Spanish and Illustrator to R. Janneke recognizes any common wild bird within 0.1 seconds.
DATA SCIENTIST
Empar Baltasar Pérez
JUNIOR DATA SCIENTIST
Empar focuses helps our customers get the most out of their data with custom data projects. She obtained an MSc in Bioinformatics and Biocomplexity at Utrecht University and a BSc degree in Biochemistry and Biomedical Sciences at the University of Valencia. Besides science, she loves listening to and playing music. She can play the flute and the piano.
JUNIOR DATA SCIENTIST
Pablo Gómez Sacristán
JUNIOR BIOINFORMATICIAN
Pablo works as a junior bioinformatician at Single Cell Discoveries and is responsible for processing and sending out data to clients. Prior to starting at Single Cell Discoveries, Pablo worked at Macrogen Europe as a Bioinformatician analyzing NGS data. He obtained both his MSc in Computational Biology and BSc in Biotechnology at the Technical University of Madrid and carried out his internships in Ireland and France. His inner nerd gets triggered by retro video games such as Pokémon and Super Mario.
JUNIOR BIOINFORMATICIAN
Sofia Drobysheva
JUNIOR DATA SCIENTIST
Sofia is working together with R&D and data teams to analyze data from mainly in-house projects. Before joining SCD, she was living in Stockholm, where she did her bachelor’s and master’s degrees, as well as working part-time in biotech start-up Capitainer. During her master’s project, she has integrating single-cell datasets. Her bachelor’s project focused on yeast with impaired Ca2+ homeostasis. In her free time, Sofia goes on long city walks or hikes.
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.