Bioinformatics services for transcriptomic, spatial, and digital pathology data
Explicyte's bioinformatics team analyzes datasets generated with us or elsewhere, from data QC and preprocessing through statistical, single-cell and spatial analysis, with biological interpretation and publication-ready outputs.
Recent papers involving our data science team
Fast, expert analysis — from raw data to biology
How we work
Fast turnaround
4 weeks to a custom data-analysis report, with shorter timelines for focused packages.
Scientists, not just scripts
We automate wherever it adds speed and consistency; biological interpretation stays with experienced bioinformaticians.
Deep FFPE experience
Extensive experience analyzing FFPE-derived transcriptomic, spatial and digital-pathology datasets across oncology studies.
BIOINFORMATICS SERVICES
Choose the analysis workflow for your data
Single-cell & spatial
10x Genomics single-cell & spatial data analysis
Chromium X, Visium HD, Xenium and Atera datasets — from data QC and preprocessing through clustering, annotation and biological or spatial interpretation.
Bulk & region-based RNAseq
Bulk RNA-seq & GeoMx DSP
Bulk RNA-seq and GeoMx DSP datasets — from data QC and normalization through differential expression, pathway analysis, biomarker discovery and spatial interpretation.
Digital pathology
mIF & IHC image analysis
Digitized mIF and IHC slides — image QC, tissue and cell segmentation, ML-assisted phenotyping, quantitative biomarker analysis and spatial analysis.
Why Explicyte
A foundation you can trust
A dedicated data science team
Experienced bioinformaticians work across transcriptomics, single-cell, spatial biology and digital pathology, with scientific oversight throughout the project.
Analyze data from any source
We work with datasets generated by Explicyte, your own laboratory, a core facility or another provider, and can incorporate public reference datasets where rele
Platform-aware QC & reproducible analysis
Analysis workflows are adapted to each data type, with quality control, preprocessing and batch-effect assessment or correction where appropriate.
Publication-ready outputs
Deliverables can include processed datasets, quantitative analyses, clear visualizations, structured reports and publication-ready figures.
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
Contact our team
Discuss your data-analysis project
Tell us the data type, files available, cohort size and biological question. A bioinformatician will review your dataset and help define the appropriate analysis scope, timeline and deliverables.
Answers about bioinformatics consulting services
Frequently asked questions
What data types can you analyze?
We analyze bulk RNA-seq, GeoMx DSP, Chromium X, Visium HD, Xenium and Atera datasets, as well as digitized mIF and IHC slides. Depending on the platform and study scope, analysis can include data QC, preprocessing, normalization or segmentation, clustering, annotation, differential analysis, spatial analysis and biological interpretation.
Can you analyze datasets generated outside Explicyte?
Yes. Our analysis is available standalone, so we can work on data generated by your team, a core facility, or another provider. We regularly pick up already-generated data for expert interpretation.
Do you support FFPE-based studies?
Yes. Our team has extensive experience with transcriptomic, spatial and digital-pathology datasets derived from FFPE material, and adapts QC, preprocessing and interpretation to the specific quality constraints of archival tissue.
How long does a project take?
It depends on dataset type, study complexity, and depth of analysis. As a general rule we aim to deliver a custom report within 4 weeks, with shorter timelines for focused packages.
Do you combine automated workflows with expert interpretation?
Yes. We use automated and machine-learning-based methods where they improve speed, consistency or analytical performance, while dataset review and biological interpretation remain under the responsibility of experienced bioinformaticians.
Do you provide publication-ready outputs?
Yes. Deliverables can include structured reports, clear visualizations, publication-ready figures, and processed datasets to support internal decisions, partner discussions, abstracts, or manuscripts.
Can you adapt the analysis to our scientific objectives?
Yes. We don’t apply one fixed workflow. We shape the analysis around your study design, dataset structure, scientific question, timeline, and reporting needs — biomarker discovery, treatment-response analysis, spatial interpretation, or figure generation.
Who do you work with?
Biotech, pharma, academic teams, and translational research groups needing fast, expert analysis of transcriptomic and digital pathology datasets.
