A quest for the real biology in your data.
OmicsQuest is an on-demand bioinformatics service for single-cell, spatial, multi-omics and imaging data. A bioinformatician and a cell biologist take your project from raw files to publication-quality figures, from $79/hour.
No hiring, onboarding or idle salary. Mutual NDA before data transfer, unlimited figure customization, and you own every result, line of code and figure.
Trusted by researchers at leading universities in the US, UK, Germany and China
- Harvard University
- Stanford University
- MIT
- Johns Hopkins University
- UC San Francisco
- Yale University
- Columbia University
- University of Pennsylvania
- University of Oxford
- University of Cambridge
- Imperial College London
- University College London
- King's College London
- University of Edinburgh
- Heidelberg University
- LMU Munich
- Technical University of Munich
- Charité Berlin
- Tsinghua University
- Peking University
- Fudan University
- Zhejiang University
- Shanghai Jiao Tong University
See the tissue and its transcriptome, cell by cell
Drag across the section. On the left, the H&E stain a pathologist reads. On the right, the same 700 × 450 µm of breast cancer measured with 10x Atera whole-transcriptome in situ profiling: every segmented cell, colored by its annotated type and registered to the H&E.
H&EAtera, single cells
- High-grade DCIS (11q13)
- Luminal-like DCIS
- Basal-like DCIS
- Myoepithelial cells
- Cancer-associated fibroblasts
- CXCL14+ fibroblasts
- Pericytes
- Endothelial cells
- T cells
- Macrophages and dendritic cells
- Plasma and mast cells
- Apocrine cells
FFPE breast cancer, ductal carcinoma in situ. 170,057 cells profiled across 18,028 genes; cell types as annotated by 10x Genomics. Data: 10x Genomics Atera preview dataset, CC BY 4.0.
In situ (Xenium and Atera) analysis · Visium HD analysis · Choosing a spatial platform
You need a bioinformatician for six weeks, not six years.
Most labs generate data in bursts, across several technologies. A full-time hire is slow to recruit, expensive between datasets, and rarely an expert in every modality you use.
Hiring in-house
- Three to six months to recruit, then onboarding
- $130,000 to $190,000 a year fully loaded in the US, busy or not
- One person rarely covers single-cell, spatial, proteomics and imaging
- When they leave, the know-how and often the code leave too
- Biology review depends on whoever has time
An OmicsQuest duo team
- Starts within a week of a free scoping call
- From $79/hour, only for the hours you use, with a capped estimate
- Specialists for each omics discipline on one team
- Reproducible code, documented methods, and you own everything
- A cell biologist checks that every result makes biological sense
Compare hiring, core facilities and on-demand teams in detail
Two experts on every project: one for the code, one for the biology.
Most failed analyses we rescue have no coding errors. They have biology errors: doublets named as new cell types, stress responses read as treatment effects, panels that cannot see the cells in question. Our duo model is built to catch them.
Bioinformatician
Pipelines, statistics, reproducibility
Chooses and benchmarks methods, models your experimental design correctly, writes versioned code, and makes sure every number in the figure can be regenerated.
Cell biologist
Context, annotation, interpretation
Reads your experiment like a reviewer, annotates cell states from biology rather than cluster numbers, flags implausible results early, and shapes the figure story.
Services by omics discipline
Every service lists the analyses we run, the deliverables, and the mistakes we design against. Browse all services.
Single-cell and epigenomics
- Single-cell RNA-seq analysisscRNA-seq and snRNA-seq: QC, integration, annotation, pseudobulk DE, trajectories.
- snATAC-seq and scATAC-seq analysisChromatin accessibility per cell type: peaks, motifs, footprints, enhancer-gene links.
- Multiome and CITE-seq analysis10x Multiome, CITE-seq, TEA-seq, DOGMA-seq: joint embeddings and regulatory networks.
- TCR/BCR immune repertoire analysisClonotypes, clonal expansion, diversity, SHM and lineage trees, linked to cell state.
- CRISPR screen and Perturb-seq analysisPooled screens and single-cell perturbation screens: hits, effects, programs.
Spatial biology
- Visium HD spatial analysis2 µm bins to cells: segmentation, deconvolution, domains, niches, signaling.
- Xenium in situ analysisRe-segmentation, transcript QC, annotation, neighborhoods and niches.
- Spatial omics (CosMx, MERSCOPE, GeoMx, CODEX)CosMx, MERSCOPE, GeoMx, Stereo-seq, CODEX, IMC: one analysis framework.
Bulk sequencing and genomics
- Bulk RNA-seq analysisDE, batch handling, pathways, isoforms, splicing, deconvolution, time courses.
- ChIP-seq, CUT&RUN and ATAC-seqPeak calling, differential binding, motifs, super-enhancers, integration.
- WGS, WES and variant analysisGermline and somatic variants, CNV, SV, GWAS, long reads.
- Metagenomics and microbiome16S/ITS, shotgun, MAGs, functional profiles, compositional statistics.
Proteomics and interactions
Imaging and phenomics
Target and drug discovery
TargetQuest: target discovery on a Virtual Human of 50 million+ cell and spatial profiles
Coordinated AI agents, supervised by our scientists, test candidate targets against genetics, cell and niche specificity, causality, druggability and safety. Then falsification agents try to break every claim. You receive a short, evidence-backed list and the experiment that would test each target best.
Virtual Human substrate: 50 million+ single-cell and spatial profiles
From raw data to publication-quality figures
One process for every discipline. You see a QC report before the main analysis, and interim figures before anything is final.
Scoping call
Thirty minutes, free. We learn the biology, the design and the deadline.
Capped estimate
A written plan with hours, deliverables and a cap. No surprise invoices.
Secure transfer and QC
Encrypted transfer, then a QC report and a go/no-go call within days.
Analysis with check-ins
Weekly calls with your duo team and interim figures you can steer.
Figures, methods, code
Publication-quality figures, methods text and reproducible code. Revisions are unlimited.
Transparent pricing, from $79 an hour
Pay for analysis by the hour, reserve a team each month, or let us build and maintain your pipelines for a flat fee. Full pricing and typical project costs.
On-demand analysis
For labs with data and a question.
$79 / hour
Starting rate. Capped estimate before work begins.
- Bioinformatician and cell biologist duo team
- Raw data to publication-quality figures
- Unlimited figure customization
- Methods text and reproducible code
- Reviewer responses and re-analysis
Embedded duo team
For groups with a steady flow of data.
$79 / hour, reserved monthly
Reserve 20, 40 or 80 hours a month.
- The same duo team on every project
- Priority turnaround and weekly meetings
- Unused hours roll over one month
- Shared project board and data catalog
- Ideal for core-less labs and biotechs
Pipelines for new labs and startups
For teams that need infrastructure, not just answers.
$1,490 / month
Flat-rate maintenance after a fixed-price build.
- Nextflow or Snakemake pipelines on your cloud or HPC
- Containers, tests and CI, so results never drift
- Updates, monitoring and new modules
- Analysis hours from the same team
- You own every line of code
Projects we rescued
Analyses that failed review, misled a program or could not be reproduced, and what fixed them. All case studies.
Guides from our analysts
Best-practice workflows and the mistakes we see most. All guides.
- Single-cell
Single-cell RNA-seq analysis: a best-practice workflow from FASTQ to figures
A step-by-step scRNA-seq workflow: alignment, empty droplets, ambient RNA, doublets, QC, integration, annotation, pseudobulk DE and trajectories.
- Single-cell
12 mistakes that ruin single-cell RNA-seq analyses, and how experts avoid them
The scRNA-seq errors we fix most: pseudoreplication, doublets called new cell types, ambient RNA, over-integration, fixed QC cutoffs, UMAP myths.
- Buying guide
How much does bioinformatics analysis cost? A 2026 pricing guide
2026 costs for scRNA-seq, RNA-seq, Visium HD, Xenium, ATAC-seq and Cell Painting analysis, and how hourly, per-sample and salary pricing compare.
- Spatial
Visium HD vs Xenium vs CosMx vs MERSCOPE: choosing a spatial transcriptomics platform
Visium HD, Xenium, CosMx, MERSCOPE and GeoMx compared: resolution, gene coverage, sample types, analysis challenges and which to choose.
- Single-cell
Pseudobulk differential expression in single-cell RNA-seq: why cells are not replicates
Why cell-level tests produce false positives in scRNA-seq, how pseudobulk aggregation works, when to use mixed models, and a practical DESeq2/edgeR workflow.
- Spatial
Visium HD data analysis: from 2 µm bins to cells, domains and niches
How to analyze Visium HD: QC and tissue masking, 8 µm bins vs nucleus segmentation, RCTD or cell2location deconvolution, domains and niches.
Questions labs ask us first
More answers on the FAQ page.
What is OmicsQuest?
OmicsQuest is an on-demand bioinformatics services company, working like a CRO for labs and biotechs. We analyze single-cell, spatial, multi-omics, bulk sequencing, proteomics and imaging data. Every project is handled by a duo team of a bioinformatician and a cell biologist, from raw data to publication-quality figures, starting at $79/hour.
How much does bioinformatics analysis cost?
OmicsQuest bills from $79/hour, and every project starts with a capped estimate. Typical ranges: bulk RNA-seq differential expression takes 8-20 hours ($632-$1,580), a 4-8 sample single-cell RNA-seq project 25-45 hours ($1,975-$3,555), and a Visium HD project 35-70 hours ($2,765-$5,530). See the pricing page for more.
Should I hire a bioinformatician or outsource?
Hire when you have more than about 1,500 hours of analysis a year in one discipline, plus the time to recruit and manage. Most labs need a few hundred hours a year across several data types. At that volume, on-demand duo teams are faster to start, cover more omics, and cost a fraction of a fully loaded salary. Read the full comparison.
What data types do you analyze?
Single-cell RNA-seq and snRNA-seq, snATAC-seq, 10x Multiome, CITE-seq, TCR/BCR repertoires, CRISPR and Perturb-seq screens, Visium HD, Xenium, CosMx, MERSCOPE, GeoMx, CODEX, bulk RNA-seq, ChIP-seq, CUT&RUN, ATAC-seq, methylation, WGS/WES, metagenomics, mass spectrometry proteomics, protein-protein interactions, Cell Painting, high-content screening and live-cell imaging.
What does unlimited figure customization mean?
Once an analysis is delivered, restyling figures for a journal, a grant or a talk costs nothing: colors, labels, layouts, panel order, fonts and formats. New analyses are scoped and billed at the same hourly rate, and you can request as many as you need.
How fast can you start?
Usually within a week of the scoping call. QC reports typically arrive 3-5 business days after data transfer. We offer expedited timelines for reviewer deadlines.
Is my data secure, and who owns the results?
We sign mutual NDAs before transfer, use encrypted transfer and storage, and can work inside your own cloud account. You own all data, results, code, figures and any intellectual property. We delete project data on request or at project close.
Do you work with startups and new labs?
Yes. Besides analysis, we build scalable, reproducible pipelines (Nextflow or Snakemake, on your cloud or HPC) and maintain them for a flat monthly fee, starting at $1,490/month. See pipelines.
Tell us about your data.
Send a few lines about your experiment. A bioinformatician and a biologist will review it and reply with questions or a capped estimate. Analysis starts at $79/hour, and figure customization is unlimited.
- Free 30-minute scoping call
- Capped estimate before any billable work
- You own all data, code, figures and IP
Prefer email? contact@omicsquest.com