Explicyte provides standalone 10x Genomics data analysis services for industry sponsors and academic teams working with Chromium X, Visium HD, and Xenium datasets. As a 10x Genomics-certified provider, we deliver fast, scientist-led bioinformatics workflows covering QC, preprocessing, annotation, spatial and single-cell interpretation, and publication-ready reporting.
- Fast turnaround: receive your custom data analysis report within 4 weeks.
- Reliable analysis pipeline: proprietary workflows for dataset cleaning, QC, & annotation.
- Human expertise, not just AI: each dataset is interpreted by an experienced bioinformatician.
- Proven track record in FFPE transcriptomics: transcriptomic datasets and figures published in top oncology journals.
Our proprietary analysis pipeline ensures fast, robust, and reproducible processing of single-cell and spatial transcriptomics datasets.
Our pre-processing workflow:
- removes technical artefacts (ambient RNA, doublets, low-quality cells)
- corrects batch effects across samples
- filters low-complexity or damaged cells
- detects and removes contaminating cell populations
- ensures reproducible and standardized preprocessing
- delivers analysis-ready single-cell datasets
Xenium dataset: cluster annotation before and after application of our preprocessing workflow.
Primary analysis
1 week
- Genome mapping and quality control
- Alignment of reads to the reference genome
- Generation of raw and filtered gene count matrices
- Mapping statistics and sequencing metrics
- Detection of low-quality barcodes and empty droplets
- Comprehensive QC report of mapping results
Deliverables
- Processed gene count tables
- Mapping and sequencing quality metrics
- Initial dataset summary
How do I transfer my transcriptomic dataset?
You can upload either raw sequencing data or processed outputs to our secured infrastructure (EU-based servers, AES-encrypted storage, high-speed transfer).
What are the accepted file formats?
- Raw sequencing files (FASTQ) for scRNA-seq and 10x Genomics Visium
- 10x Genomics output folders (Cell Ranger / Space Ranger results)
- Xenium Ranger outputs for spatial transcriptomics
- Optional: sample metadata file (experimental conditions, batches, clinical annotations)
Dataset annotation
2 weeks
- Level 1 + full dataset preprocessing
- Removal of low-quality cells and technical artefacts
- Doublet detection and removal
- Optimized cell segmentation (Xenium)
- Cell clustering and dimensionality reduction (UMAP/t-SNE)
- Automated cell type annotation using AI-assisted tools and curated reference databases
Deliverables
- Cleaned and normalized dataset
- Annotated cell clusters
- Clustering visualizations
- Intermediate analysis report
Advanced analysis
4 weeks
- Level 2 + Comprehensive biological interpretation
- Differential gene expression analysis (clusters/conditions)
- Gene set enrichment and pathway analysis
- Cell population comparison across samples
- Identification of marker genes and functional signatures
- Publication-ready figures and summary report
Deliverables
- Full analytical report
- Ready-to-publish high-quality figures
- All processed data files
Ask us about additional analysis strategies:
- Gene regulatory networks
- Trajectory analysis (pseudotime and velocity)
- Integrative single-cell analysis (multiple datasets, public data, cell atlas, multi-omics analyses)
Deliverables
- Cell Ranger outputs and FASTQ files
- Fully processed gene expression matrix (raw and filtered count tables)
- Quality control report (sequencing metrics, cell filtering, dataset statistics)
- Cleaned and normalized single-cell dataset
- Cell clustering and dimensionality reduction visualizations (UMAP / t-SNE)
- Cell type annotation using curated reference databases and AI-assisted tools
- Cluster marker gene identification
- .cloupe file for easy visualization with the 10x Genomics Loupe Browser
- Publication-ready figures and analysis report
Deliverables
- Space Ranger outputs and FASTQ files
- Processed spatial gene expression matrices
- Quality control report (sequencing metrics, spot filtering, dataset statistics)
- Spatial clustering and tissue domain identification
- Spatially variable gene detection
- Cell type mapping using reference single-cell datasets
- Spatial visualization of gene expression and cell populations
- High-resolution microscopy images
- CytAssist images
- .cloupe file for easy visualization with the 10x Genomics Loupe Browser
- Publication-ready spatial maps and figures
Deliverables
- Xenium Ranger output
- Processed single-cell gene expression matrices
- Cell segmentation masks and cell boundary files
- Transcript coordinate tables (molecule-level spatial information)
- Cell-level metadata tables (cell area, transcript counts, QC metrics)
- Quality control report (transcript detection statistics, segmentation metrics)
- Cell clustering and cell type annotation using curated reference datasets
- Spatial mapping of cell populations within the tissue
- Cell–cell interaction and neighborhood analysis
- Spatial visualization of gene expression patterns
- High-resolution images
- CytAssist images
- Interactive visualization files compatible with Xenium Explorer
- Publication-ready spatial maps and figures
Experts
in Transcriptomic Analysis
- Certified 10x Genomics service provider across all 10x single-cell and spatial platforms
- Proprietary dataset preprocessing workflow to secure and speed up downstream analysis
- Academic track record: transcriptomic datasets and figures published in top journals
Personalized
approach
- Tailored analysis: we adapt our pipeline to your scientific question, time, and budget constraints
- Dedicated bioinformatics lead: a data scientist is in charge of your study
- Actionable HTML reports to dive into data and download publication-ready figures
Can Explicyte analyze 10x Genomics datasets generated outside Explicyte?
Yes. Our data analysis services are available as a standalone offering, meaning we can support projects even when the wet-lab work was performed by another provider, core facility, or internal team. We regularly work on externally generated datasets and adapt our analysis workflow to the project objectives, study design, and dataset quality.
Which 10x Genomics platforms do you support?
We provide bioinformatics support across the full 10x Genomics suite, including Chromium X for single-cell RNA-seq, Visium HD for spatial whole-transcriptome analysis, and Xenium for single-cell spatial transcriptomics. Our team can support each platform independently or help compare and integrate outputs across platforms when relevant to the study.
What is included in your primary analysis package?
Our primary analysis package covers the core processing steps required to convert raw data into a usable dataset. Depending on the platform, this includes alignment, generation of count matrices, sequencing and mapping QC metrics, and a first-level quality assessment of the dataset. This package is designed for teams that need robust processing and quality control before moving into biological interpretation.
What is included in your dataset annotation package?
Our dataset annotation package goes one step further by transforming processed data into an interpretable biological dataset. This typically includes preprocessing, filtering of low-quality cells or artefacts, clustering, dimensionality reduction, and cell population annotation. For Xenium datasets, this may also include optimization of segmentation and dataset cleaning prior to interpretation.
What is included in your advanced analysis package?
Our advanced analysis package is designed for teams seeking deeper biological insight. Depending on the study goals, this may include differential expression analysis, pathway and gene-set enrichment analysis, comparison between study groups, identification of relevant cellular states, and generation of publication-ready figures. We can also discuss more advanced exploratory strategies when needed.
How long does a 10x Genomics data analysis project usually take?
Timelines depend on the scope of analysis and the complexity of the dataset. As a general guide, our primary analysis is usually delivered within about 1 week, dataset annotation within about 2 weeks, and advanced analysis within about 4 weeks. For larger or more complex projects, we define a tailored timeline at project kickoff.
Do you provide publication-ready figures and reports?
Yes. We aim to deliver outputs that are not only technically robust, but also directly usable by scientific teams. Depending on the selected package, deliverables can include clear visualizations, annotated figures, and structured reports that support internal decision-making, partner discussions, conference abstracts, or manuscript preparation.
Is your analysis fully automated?
No. While we use robust computational workflows and state-of-the-art tools, our analyses are not purely automated. Each project is reviewed and interpreted by an experienced data scientist, with oversight tailored to the scientific question being addressed. We believe expert interpretation is essential to generate biologically meaningful conclusions from complex transcriptomic datasets.
Can you adapt the analysis to our scientific question?
Yes. We do not apply a one-size-fits-all workflow. Our analysis strategy is tailored to your study objectives, the type of dataset generated, and the level of depth required. Whether your goal is to characterize cell populations, compare treatment groups, identify biomarkers, or generate figures for publication, we adapt the analysis plan accordingly.
Do you support FFPE transcriptomics projects?
Yes. We have strong experience working with FFPE-derived transcriptomic datasets, including spatial and targeted transcriptomics approaches. Our team is familiar with the specific challenges associated with FFPE material and can help extract robust biological insight from these datasets.
Can you integrate multiple datasets in the same project?
Yes. When relevant, we can integrate multiple datasets within the same analysis framework. This may include combining several single-cell datasets, comparing multiple Xenium samples, or integrating internal data with public references or cell atlases. The objective is always to improve biological interpretation and strengthen the relevance of the conclusions.
Who is this service for?
Our 10x Genomics data analysis services are designed for biotech companies, pharmaceutical companies, academic teams, and translational research groups that need rapid, expert interpretation of complex transcriptomic datasets. We support both teams looking for a full bioinformatics partner and groups needing targeted support on specific datasets.
Why work with Explicyte for 10x Genomics data analysis?
We combine 10x Genomics-certified expertise, a dedicated bioinformatics team, experience in single-cell and spatial transcriptomics, and a strong track record in translational oncology and FFPE-based projects. Our goal is to deliver analyses that are scientifically rigorous, operationally efficient, and directly aligned with the decisions our clients need to make.
Talk to our team
Talk to our team !
Paul Marteau, PharmD (preclinical study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)