From Data to Discovery
Your Bioinformatics Partner
We deliver reproducible, publication-style analyses with full source code and methods across transcriptomics, genomics, proteomics, metagenomics, machine learning, and more.
- Publication-level deliverablesFigures, tables, and methods designed for manuscript inclusion
- Reproducible by designTransparent pipelines with full code and methodology
- Dedicated scientific partnerWeekly updates and milestone-based project management
What does Pepkio offer as a bioinformatics CRO?
Pepkio is a full-service bioinformatics contract research organization covering nine analysis areas with milestone-based pricing, publication-style deliverables, and full code handover on every project.
| Fact | Detail |
|---|---|
| Service coverage | Nine analysis areas: transcriptomics, genomics, proteomics, metagenomics, metabolomics, machine learning, statistical modeling, custom analysis, and consulting |
| Deliverables | Publication-style figures and tables, commented R/Python workflows, methods drafts, and version-pinned environments |
| Pricing model | Fixed milestone-based pricing with defined deliverables per phase — no open-ended hourly billing |
| Client ownership | 100% client ownership of all code, scripts, processed data, and analysis results |
| Scientific team | 30+ senior bioinformaticians with experience across academia, biotech, and pharma |
Researching whether to outsource? Browse our buyer-education guides.
Common questions before you outsource bioinformatics
Short answers to the decisions most labs research first. Full guides live in our buyer-education resource centre.
How do I choose a bioinformatics CRO?
Choosing a bioinformatics CRO means evaluating whether an outsourced team can deliver reproducible, manuscript-ready analyses—not just raw gene lists.
Should I outsource bioinformatics or hire in-house?
Outsource or hire?
How much does bioinformatics analysis cost?
Bioinformatics analysis cost varies with project scope, complexity, and provider type.
Why does reproducibility matter when outsourcing?
Publication-ready bioinformatics means a colleague or peer reviewer can rerun your analysis from the same inputs and get the same results.
What are red flags when evaluating a bioinformatics CRO?
The most common warning signs when evaluating a bioinformatics CRO come down to scientific transparency.
How long does bioinformatics analysis take?
Bioinformatics turnaround depends more on provider queue and service model than on compute time alone.
What bioinformatics analysis services does Pepkio offer?
Browse nine service areas below, each page explains the methods we use and the deliverables you receive, so you can see what fits your project before reaching out.
- Transcriptomics
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- Bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics
- Cell typing, trajectory analysis, pathway enrichment
- Genomics & Variant Analysis
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- Variant calling, annotation, WGS/WES analysis
- CNV and structural variation detection
- Proteomics
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- DDA/DIA MS, single-cell proteomics, Olink NPX analysis
- Differential abundance, pathway integration, and metabolomics-ready outputs
- Metagenomics
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- 16S amplicon, shotgun metagenomics, metatranscriptomics
- Taxonomic profiling, functional pathways, and diversity analysis
- Metabolomics
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- Untargeted LC-MS/GC-MS profiling and feature annotation
- Pathway enrichment and multi-omics integration
- Machine Learning & AI
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- Predictive modeling, feature selection
- Biomarker discovery
- Mendelian Randomization & Statistical Modeling
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- Causal inference, hypothesis-driven analyses
- Data exploration
- Custom Analysis
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- Multi-omics integration, pipeline ports, novel assay QC
- Version-pinned workflows, Methods drafts, milestone delivery
- Bioinformatics Consulting
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- Experimental design, pipeline selection, feasibility review
- Knowledge transfer before you commit to sequencing or analysis
What makes Pepkio different from other bioinformatics CROs?
Unlike large CROs, we are agile, deeply engaged, and focused on long-term collaboration — an extension of your research team, not just a vendor.
Publication-style deliverables
Figures, tables, and methods designed for manuscript inclusion — not slide-deck summaries.
Reproducible by design
Transparent pipelines with full code and methodology. No black-box deliverables.
Dedicated scientific partner
PhD-level scientific contact, weekly updates, and thought partnership — not order-taking.
Milestone-based pricing
Fixed deliverables and timelines per phase. No surprise costs or open-ended billing.
Reviewer support and data security
Clarification support for peer review, encrypted data transfer, NDAs, and GDPR-aware workflows.
How does Pepkio deliver a bioinformatics project?
A transparent, collaborative workflow from biological briefing through delivery and reviewer support.
Wondering how long each phase takes? See realistic timelines by modality →
Step 1
Biological Briefing
Understand hypothesis and study goals
Step 2
Secure Data Handling
Encrypted transfer, isolated servers
Step 3
QC & Feasibility
Check data quality before full analysis
Step 4
Primary & Custom Analysis
Reproducible pipelines with tailored visualizations
Step 5
Delivery & Support
Publication-style outputs, figure-ready plots, and reviewer support
Trusted by researchers worldwide
Last updated: · About Pepkio
- 30+
- senior bioinformaticians
- Contributions to
- peer-reviewed publications
- Experience across
- academia, biotech, and pharma
Frequently asked questions about Pepkio
Practical questions about working with Pepkio. For outsourcing decisions, see the buyer guides above; for the full service FAQ, visit our bioinformatics CRO FAQ.
Is there a minimum project size or budget required to work with Pepkio?
No. We support everything from small tasks (e.g., debugging a script or interpreting a figure) to large, multi-stage studies.
Is the free consultation focused on discussing my research, or is it just a sales call?
The consultation is research-focused. We aim to understand your scientific goals and then discuss feasibility, timelines, and cost.
How do you define "milestone-based" pricing, and when are payments triggered?
For larger projects, we define clear milestones (e.g., QC & feasibility, primary analysis, downstream enrichment, final report). An initial payment starts the project, with subsequent payments triggered upon completion of each milestone. For small or simple projects, there may be a single milestone upon project completion.
Do you require co-authorship on publications?
No. We operate strictly as a fee-for-service provider unless co-authorship is explicitly discussed in advance.
Can you run analyses inside our own servers or cloud environment (on-prem, AWS, or GCP via VPN)?
Yes. For teams that require data to stay inside their environment, we can perform remote analysis on your on-premises servers or within your AWS or GCP accounts. Access is typically established via VPN or a private network connection, with credentials and access controls managed according to your IT policies. We align on the setup during scoping so analysis runs in your infrastructure while you still receive the same reproducible deliverables and documentation.
Let's Talk About Your Science
Tell us:
- • Your biological question
- • Data type and size
- • Timeline constraints
We'll tell you:
- • What's feasible
- • How long it will take
- • Exactly what it will cost
Contact us to start with a free consultation. Need everyday bench calculators? Try our free lab tools.