Services

Professional Bioinformatics Solutions

We deliver pharma-grade bioinformatics services with reproducible workflows, comprehensive documentation, and publication-ready outputs. Every project follows industry best practices for quality, compliance, and scientific rigor.

🧬 NGS Analysis

What We Offer

Comprehensive next-generation sequencing analysis from raw data to actionable insights. We handle the entire workflow: QC, alignment, differential expression, pathway enrichment, and visualization.

Technologies Supported

RNA-seq: Bulk RNA-seq with limma-voom, edgeR, DESeq2. From FASTQ to differential expression and pathway analysis.

scRNA-seq: Single-cell analysis with Seurat/Scanpy. Cell type annotation, UMAP visualization, trajectory analysis, immune repertoire profiling (scTCR-seq, scBCR-seq).

ChIP-seq/ATAC-seq: Peak calling, motif enrichment, transcription factor binding analysis, chromatin accessibility.

CRISPR Screens: Genome-wide screens with crisprVerse, MAGeCK. Hit calling, normalization, validation strategy.

WGS/WES: Variant calling with GATK, COSMIC signature analysis, somatic mutation detection.

Spatial Transcriptomics: 10X Visium analysis, spatial gene expression, tissue architecture mapping.

Long-Read Sequencing: PacBio and Nanopore analysis for isoform detection and structural variants.

Methylation: WGBS and Infinium array analysis for epigenetic profiling.

Problem β†’ Solution

Problem: You have terabytes of FASTQ files but no in-house expertise for analysis.

Solution: We process your data end-to-end with established pipelines, delivering publication-ready results with comprehensive QC reports.

Deliverables:

  • Quarto/RMarkdown analysis reports
  • Processed count matrices and metadata
  • Publication-quality figures (heatmaps, volcano plots, UMAPs)
  • Pathway enrichment results (fgsea, MSigDB)
  • Gene lists (DEGs, biomarkers)
  • GitHub repository with reproducible code

Timeline: 2-8 weeks depending on complexity
Typical Cost: Contact for quote based on sample size

πŸ“§ Request NGS Analysis Quote

πŸ“¦ R Package Development

What We Offer

Custom R packages built to CRAN/Bioconductor standards. We transform your analysis scripts into production-ready, maintainable software with comprehensive documentation and testing.

Our Approach

1. Requirements
We work with your team to understand workflows, define functions, and plan package architecture.

2. Development
Build using devtools/usethis, roxygen2 documentation, testthat unit tests, vignettes with examples.

3. Documentation
Create pkgdown website, comprehensive vignettes, function references, installation guides.

4. Submission
CRAN/Bioconductor submission support including addressing reviewer feedback.

Problem β†’ Solution

Problem: Your team has valuable analysis code scattered across scripts that’s hard to maintain and share.

Solution: We package your code into a professional R package with documentation, testing, and a public website.

Deliverables:

  • Documented R package (roxygen2)
  • pkgdown website
  • Unit tests (>80% coverage)
  • Vignettes with worked examples
  • GitHub repository with CI/CD
  • CRAN/Bioconductor submission (optional)

Timeline: 4-12 weeks
Typical Cost: Contact for quote

πŸ“§ Discuss Package Development

βš™οΈ Pipeline Development

What We Offer

Production-ready Snakemake and Nextflow workflows for automated data processing. Fully containerized, HPC-optimized, and documented for easy deployment.

Pipeline Features

βœ“ Automated QC β€” Built-in quality control at every step
βœ“ Containerization β€” Docker/Singularity for reproducibility
βœ“ HPC Ready β€” Optimized for cluster execution
βœ“ Scalable β€” Handle 10 or 10,000 samples
βœ“ CI/CD β€” Automated testing with GitHub Actions
βœ“ Documentation β€” Comprehensive usage guides

Problem β†’ Solution

Problem: Manual analysis is time-consuming, error-prone, and not reproducible across batches.

Solution: We build automated pipelines that process your data consistently, with built-in QC and containerization.

Deliverables:

  • Snakemake/Nextflow pipeline code
  • Docker/Singularity containers
  • Configuration files for HPC
  • Comprehensive documentation
  • Example datasets and outputs
  • GitHub repository with CI/CD

Timeline: 4-12 weeks
Typical Cost: Contact for quote

πŸ“§ Request Pipeline Consultation

πŸ€– AI System Deployment

What We Offer

Machine learning model development and deployment for genomics applications. From feature engineering to production REST APIs with monitoring.

AI Capabilities

Feature Engineering: Transform raw genomic data into ML-ready features with proper normalization and batch correction.

Supervised Learning: Classification (PAM, random forests, neural networks) and regression for biomarker discovery.

Unsupervised Learning: Consensus NMF for subtype discovery, clustering for patient stratification.

Model Validation: Cross-validation design, independent cohort testing, clinical performance metrics.

Deployment: REST APIs, automated QC systems, real-time prediction services.

Problem β†’ Solution

Problem: You have ML models in Jupyter notebooks but need production deployment for clinical use.

Solution: We transform research models into production systems with proper validation and deployment infrastructure.

Deliverables:

  • ML-ready datasets (balanced, normalized)
  • Trained models with validation results
  • REST API for predictions
  • Model monitoring dashboard
  • Deployment documentation
  • Performance reports

Timeline: 6-16 weeks
Typical Cost: Contact for quote

πŸ“§ Discuss AI Integration

πŸ“Š Shiny Dashboards

What We Offer

Interactive Shiny applications for data exploration, QC monitoring, and client-facing visualizations. Deployed on shinyapps.io, RStudio Connect, or GitHub Pages.

Dashboard Types

QC Monitoring
Real-time sequencing quality control with automatic alerts for failed samples.

Data Exploration
Interactive UMAP/volcano plot explorers with gene filtering and pathway lookup.

Drug Response
Visualization of compound screening results with dose-response curves.

Custom Tools
Tailored dashboards for your specific analysis needs and workflows.

Problem β†’ Solution

Problem: Static PDFs don’t allow clients to explore their data interactively.

Solution: We build intuitive Shiny apps that let users explore results, filter genes, and export custom plots.

Deliverables:

  • Deployed Shiny application
  • Source code (GitHub)
  • User documentation
  • Admin panel (if applicable)
  • Training materials

Timeline: 2-6 weeks
Typical Cost: Contact for quote

πŸ“§ Request Dashboard Demo

πŸ”¬ Multi-Omics Integration

What We Offer

Integrated analysis of transcriptomics, genomics, and epigenomics data. We combine multiple data types to provide comprehensive biological insights.

Integration Capabilities

Data Harmonization: Integrate RNA-seq + WGS + methylation + clinical data with proper normalization.

Public Data Mining: TCGA, GEO, EGA integration for meta-analysis and validation.

Pathway Analysis: Multi-omics pathway enrichment to identify key regulatory mechanisms.

Network Analysis: Regulatory network reconstruction from multi-omics data.

Clinical Correlation: Link omics features to patient outcomes and treatment response.

Problem β†’ Solution

Problem: You have multiple data types (RNA, DNA, methylation) but don’t know how to integrate them meaningfully.

Solution: We combine datasets with proper normalization, identify multi-omics biomarkers, and build predictive models.

Deliverables:

  • Integrated data matrices
  • Multi-omics analysis report
  • Pathway enrichment results
  • Network visualizations
  • Biomarker candidates
  • Statistical validation

Timeline: 4-12 weeks
Typical Cost: Contact for quote

πŸ“§ Discuss Multi-Omics Project

πŸ’Ό Additional Services

Publication Support

Methods Sections: We write comprehensive Methods sections with all statistical details.

Supplementary Analyses: Additional analyses requested by reviewers, sensitivity analyses.

Publication Figures: High-resolution, journal-ready figures meeting specific requirements.

Timeline: 1-4 weeks
Request Support β†’

Training & Workshops

R/Bioconductor Training: Hands-on workshops for your team on NGS analysis, package development.

Pipeline Training: How to use and customize Snakemake/Nextflow workflows.

Best Practices: Reproducible research, version control, documentation standards.

Timeline: 1-3 days
Inquire About Training β†’

πŸ“‹ Our Process

1. Discovery Call

Duration: 30-60 minutes

We discuss your project requirements, timeline, budget, and expected deliverables. Free initial consultation.

Schedule Call β†’

2. Proposal & Quote

Duration: 3-5 business days

Detailed proposal including scope of work, timeline, milestones, and cost breakdown.

3. Contract & Kickoff

Duration: 1 week

NDA signing (if needed), contract finalization, data transfer setup, project kickoff meeting.

4. Analysis & Development

Duration: Project-specific

Regular progress updates (weekly or bi-weekly), milestone reviews, iterative feedback.

5. Delivery & Support

Duration: Ongoing

Final deliverables, documentation, presentation, and 30 days of post-project support included.

❓ Frequently Asked Questions

What file formats do you work with?

FASTQ, BAM, VCF, h5ad, Seurat objects, CSV/TSV, Excel, and most standard genomics formats. We can also work with proprietary formats from sequencing platforms.

Do you sign NDAs?

Yes, we routinely sign NDAs for confidential projects and can accommodate specific legal requirements.

Can you work with clinical trial data?

Absolutely. We have 9+ years of experience analyzing clinical trial data at Roche, including OAK, POPLAR, and other Phase II/III trials.

What about data security?

All data transfers are encrypted. We can work with your secure data environment or use approved cloud solutions (AWS, Azure, Google Cloud).

Do you provide long-term support?

Yes. After project completion, we offer maintenance contracts for pipelines, package updates, and ongoing analysis support.

Can you work with our existing tools?

Yes. We integrate with your existing infrastructure and can adapt to your preferred technologies and workflows.

πŸš€ Ready to Start?

Let’s discuss your bioinformatics needs

Whether you need a one-time analysis or ongoing partnership, we’re here to help accelerate your research with pharma-grade bioinformatics.

πŸ“§ Contact Us Today πŸ’Ό LinkedIn Message

Email: kontakt@actn3.pl
Response Time: Within 24 hours