Services & Capabilities
Flexible engagement models across computational analysis, workflow engineering, and scientific software development. Built for reproducibility, transparency, and acceleration of biological insight.
1. Analysis Execution
End-to-end processing from raw data (FASTQ / BAM / matrices) to annotated results.
RNA-seq (Bulk)
- QC, trimming, alignment / pseudo-alignment
- Differential expression (counts normalization)
- Pathway / enrichment analysis
- Publication-ready figures
Single-cell RNA-seq
- Filtering, normalization, clustering
- Marker gene identification
- Trajectory / pseudotime (optional)
- Cell type annotation framework
Metagenomics / Microbiome
- Taxonomic profiling
- Diversity metrics & ordination
- Differential abundance
- Pathway inference (optional)
WGS / WES
- Alignment & variant calling
- Annotation (SNVs / Indels)
- Variant prioritization
- Summary reports
ATAC / ChIP-seq
- Peak calling & QC
- Differential accessibility / binding
- Motif enrichment
- Integration with RNA-seq
Methylation / Epigenomics
- Bisulfite alignment & calling
- Differential methylation
- Integration with expression
- Region annotation
2. Pipelines & Workflow Engineering
Production-grade, reproducible workflows emphasizing modularity, provenance, and scalability.
Pipeline Development
- Snakemake / Nextflow / CWL
- Docker / Singularity environments
- Parameter schema & validation
- Automated testing hooks
Pipeline Modernization
- Legacy bash → modular framework
- Runtime & cost optimization
- Logging & audit trails
- Artifact version tracking
Cloud Orchestration
- AWS Batch / Lambda / Step Functions
- Spot cost strategies
- Secure data staging
- CI/CD integration
3. Custom Software & Tools
Interfaces and services that make data consumable for scientists and stakeholders.
Dashboards & Portals
- Secure auth & roles
- Interactive visualization
- Audit logging
- Export functions
APIs & Data Services
- REST / GraphQL endpoints
- Structured data access
- Token-based authorization
- Documentation bundles
Utilities & Tooling
- CLI & desktop tools
- ETL pre-processing
- Results packaging
- Report automation
4. Advisory & Embedded Support
Strategic guidance or integrated capacity extension.
Architecture Reviews
- Workflow design assessments
- Scalability & reliability
- Security posture checks
- Gap remediation plan
Optimization Audits
- Runtime profiling
- Cost reduction tactics
- Resource scaling
- Benchmark comparisons
Embedded Partner
- Fractional bioinformatics engineer
- Mentoring & enablement
- Backlog execution
- On-call advisory
Engagement Models
- Project Based: Defined deliverables, timelines, and hour allocation. Flat fee.
- Retainer: Revolving monthly time commitment for iterative needs.
- Hourly Advisory: Targeted troubleshooting / mentoring.
Have a dataset or workflow in mind?
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