Data Consulting 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
Every service includes a set of standard deliverables, ensuring that any scientist can quickly begin 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 file 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
For Discovery-seq data analysis, we deliver:
- Raw sequencing data (FASTQ files)
- Gene count tables
- QC report of mapping results (UMIs per sample)
- An explanation from our data team about data quality metrics
For Visium HD data analysis, we deliver:
- Raw sequencing data (FASTQ files)
- High-resolution microscopy images
- CytAssist images
- Feature barcode matrices in H5 format for 2, 8, and 16 µm bins
- A cloupe file for easy visualization with the 10x Genomics Loupe Browser
- An interactive exploratory data analysis report
- An explanation from our data team about data quality metrics
- A Seurat object to do your own analysis with the Seurat spatial workflows
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.
Bespoke data consulting
Our data scientists can maximize your biological discovery
Our data consultancy service is designed for scientists seeking easy access to deep bioinformatics expertise. Rely on us for fast, flexible analysis — whether it’s rapid, hassle-free interpretation of transcriptomic data, custom publication-ready figures, or guidance for future hypotheses. You bring the biological insight; we bring the analytical power.
It does not matter whether your transcriptome data was generated with us or somewhere else—we’re here to help uncover actionable insights. For all assays, we can:
- Perform comprehensive quality control, normalization, and batch correction as needed
- Curate data with expert, customized approaches
- Apply dimensionality reduction techniques (e.g., PCA, UMAP, PHATE) and generate intuitive visualizations
- Cluster cells or samples using unsupervised learning methods
- Conduct differential expression analysis across samples, clusters, or cell types
- Perform gene set enrichment and pathway analysis
- Produce high-resolution, publication-quality figures
- Deliver tailored analyses based on your specific goals, following a detailed consultation
Bespoke data consulting
For single-cell sequencing data analysis, we can also help you with:
- Cell type identification
- Cell label transfer using annotated, publicly available datasets
- Dataset integration, including with publicly available datasets
- Sample demultiplexing using hashtag oligos or SNPS
For bulk RNA sequencing data analysis, we can also do:
- Deconvolution of cell type abundances using single-cell reference datasets
For Discovery-seq analysis, we can also do:
- Hit identification based on candidate target genes or pathways
For Visium HD we can also help you with:
- Identification of spatially defined tissue domains
- Generation of spatially aware clusters, within or across samples
- Tissue domain annotation
- Spot deconvolution using annotated scRNAseq reference datasets
- Integration with single-cell datasets
THE DATA SCIENCE TEAM
Meet our experts
Click on a profile to read more personal info.
Regan Hamel
HEAD OF DATA SCIENCE
Regan Hamel, PhD is Head of Data Science at Single Cell Discoveries, where she leads a team of bioinformaticians in applying advanced analytical techniques to process and interpret transcriptomic data. She built her first single-cell atlas as a wet lab scientist during her PhD at the University of Cambridge and later transitioned to industry as a bioinformatician and project lead in R&D for a cell-reprogramming biotech. At SCD, she guides her team in delivering actionable insights for clients, helping them navigate complex biological data to drive scientific discovery. In her spare time, Regan enjoys working out and exploring Europe by train. HEAD OF DATA SCIENCE
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.
DATA SCIENTIST
Gini Smit
DATA SCIENTIST
Gini Smit joined SCD as an R&D Scientist helping to develop Discovery-seq before transitioning to Data Science consultancy. As a Data Scientist, she analyzes transcriptomic datasets from clients to help them achieve valuable biological insights from their data. She obtained her BSc degree in Pharmaceutical Sciences at Vrije Universiteit and her MSc degree in Bio-Pharmaceutical Sciences at Leiden University. After that, she obtained her PhD at Leiden University, where she focused on immune responses in cardiovascular disease using single-cell RNA sequencing and flow cytometry. In her spare time, Gini enjoys cooking homestyle and haut-cuisine dishes, running and weightlifting.
DATA SCIENTIST
Pablo Gómez Sacristán
BIOINFORMATICIAN
Pablo works as a 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.
BIOINFORMATICIAN
Francesco Valzano
DATA SCIENTIST
As a data scientist, Francesco's primary focus will be analyzing transcriptomic data from customers and translating these data into biological insights.
He is a trained pharmacist, but his curiosity about biology led me to pursue a PhD in Molecular Medicine at the University of Graz, followed by a postdoc in bioinformatics at the Prinses Máxima Centrum. During these roles, he focused on pulmonary vascular diseases and pediatric neuro-oncology. Through these experiences, he gained extensive expertise in transcriptomic data analysis and the interpretation of results. His hobbies include cooking, playing tennis, and riding motorbikes.
DATA SCIENTIST
Tiago Figueiredo
BIOINFORMATICIAN
Tiago is a Bioinformatician at Single Cell Discoveries, where he processes and analyzes transcriptomic data to ensure clients receive high-quality results. He enjoys developing custom scripts to improve workflows and streamline data analysis. Tiago finds the creative side of programming rewarding, breaking down complex challenges into manageable pieces and tackling errors like a detective. His passion for bioinformatics began during his Master's in Health Sciences at the University of Minho, where he analyzed transcriptomic data from malaria parasites. He expanded his expertise during an Erasmus traineeship at Stockholm University, studying octopus transcriptomes. Outside of work, Tiago is a first-class geek who enjoys bouldering (mostly falling), cooking, watching movies, and playing video games.
BIOINFORMATICIAN
How can we help?
Want to supercharge your project with our bespoke data consulting?
Connect with our PhD-level scientists to discuss your project.