Your Bioinformatics Team, Powered by AI
You focus on the science. We deliver validated, publication-ready results. AlignMatrix combines domain expertise with AI-powered analytical pipelines to transform your transcriptomic data into actionable biological insights.
From Raw Data to Biological Insights
Complex transcriptomic experiments demand more than automated pipelines. They require expert judgment at every step.
Validated Methodology
Our immune profiling pipeline ranked #5 in the DREAM Tumor Deconvolution Challenge. Every method implements peer-reviewed, field-standard approaches.
AI-Native Platform
Our multi-agent AI framework evaluates findings from multiple analytical perspectives, cross-validating results and identifying insights single-method approaches miss.
Expert-in-the-Loop
Every analysis is reviewed by domain experts before delivery. We check for biological plausibility, flag potential artifacts, and provide interpretation context.
Three Steps to Publication-Ready Results
Submit Your Project
Tell us about your research question, dataset, and goals. We'll scope the analysis and provide a clear quote within one business day.
Expert Analysis
Our validated pipelines process your data while our multi-agent AI system evaluates results from multiple perspectives. Domain experts review every output.
Reviewed Results Delivered
Receive publication-ready figures, comprehensive reports, and expert interpretation notes. We're available to discuss findings and support your next steps.
Our Solutions
Validated analytical pipelines spanning the full transcriptomics landscape — from bulk and single-cell RNA-seq to spatial, genomics, and biological aging.
AlignRNA
End-to-end bulk RNA-seq workflow. Core: limma-voom DE + ORA/GSEA. Pro: adds DESeq2, batch correction (ComBat/sva), multi-method enrichment. Advanced: interactive Shiny UI with publication figures.
AlignCell
Single-cell RNA-seq from QC to biological insights. Full Seurat 5.0 workflow with cell type annotation, trajectory analysis, and cell-cell communication.
AlignSpace
Spatial transcriptomics for Visium and Xenium platforms. Spatial clustering, deconvolution, and tissue microenvironment characterization.
AlignImmuneScape
Resolve 29 PBMC cell types from bulk RNA-seq without single-cell experiments. DREAM Challenge validated (rank #5, r=0.693).
AlignLearn
AI-generated educational content and custom bioinformatics reports. Professional documentation in PDF, EPUB, and HTML formats.
Aligncellscape
General-purpose deconvolution from bulk RNA-seq. 24 tumor microenvironment cell types, 28 PBMC immune types, and 50 Hallmark pathways.
AlignTrackImmune
Two independent immune aging indices — Lymphoid Aging (naive T cell depletion) and Myeloid Inflammatory (GTEx-derived module) — with quadrant classification. Reference: Sound Life + GTEx v8 (n=1,015).
AlignClock
Three validated biological age clocks from bulk RNA-seq: TraMA (mortality risk), Moqri (epigenetic silencing), CV Ratio (cellular vitality). AUC up to 0.959.
AlignSkillPacks
AI skills for Claude Code, distilled from real analysis projects and iteratively refined by human experts. Battle-tested patterns for RNA-seq, scRNA-seq, Shiny, Nextflow, and LLM workflows.
AlignNFSeq
Orchestrate nf-core Nextflow pipelines from a Shiny interface. Fetch FASTQs, align with STAR+Salmon, and run DE analysis — on GCP or local Docker.
AlignSarek
R package wrapping nf-core/sarek for whole-genome and whole-exome variant calling. Interactive Shiny UI for sample configuration, pipeline launch, and monitoring.
AlignVCF
VCF annotation and analysis pipeline with dark-themed Shiny interface. Variant filtering, ClinVar/gnomAD annotation, and quality metrics visualization.
AlignClock Multimodal
Extends AlignClock beyond transcriptomics to integrate clinical laboratory values (CBC, metabolic panels) for multimodal biological age estimation.
AlignClinical
Clinical-grade bioinformatics for regulated environments. FDA/EMA compliant pipelines with complete audit trails.
AlignTarget
Biomarker discovery and drug target identification from multi-omics data. Machine learning prioritization.
Ready to Accelerate Your Research?
Submit your project details and receive a scoping proposal within one business day.