The Virtual Lab · Pipelines
Every pipeline is delivered today as an scientist-led project. Methods are named so you can judge them. The status column says which are also being wrapped by a scoped agent.
Standard catalogue
| Pipeline | Methods | Status |
|---|---|---|
| Single-cell RNA-seq | MAD-based QC; doublet detection; scVI/scANVI integration; annotation; pseudobulk differential expression by donor (no pseudoreplication); trajectory | Scientist-led |
| Bulk RNA-seq | Alignment and quantification; DESeq2 / edgeR; fgsea / GSEA over MSigDB (H, C2, C3, C5, C6, C7); deconvolution | Scientist-led |
| CITE-seq | totalVI on raw counts; joint protein–RNA analysis; surface-marker validation of transcriptional clusters | Scientist-led |
| WES / WGS | Somatic SNV/indel/CNV/SV (tumour–normal and tumour-only); germline; nf-core/sarek where applicable | Scientist-led · agent in development |
| scATAC / multiome | PeakVI, snapATAC2, MultiVI; motif and gene-regulatory-network inference | Planned |
| Single-cell DNA | Mission Bio Tapestri genotyping; clone calling; co-occurrence | Scientist-led |
| Spatial transcriptomics | Deconvolution (DestVI); niche analysis; cell–cell interaction | Planned |
| Targeted panels | Variant calling; interpretation against ACMG/AMP, OncoKB, COSMIC, gnomAD; TP53 mono- vs bi-allelic state | Scientist-led · agent in development |
| Methylation | EPIC array; EM-seq / RRBS; DMR calling | Planned |
| Long-read | ONT / PacBio isoform analysis; structural variants; phasing | Planned |
| Immune repertoire | BCR/TCR clonotyping; diversity; clonotype tracking (shared machinery with MRD) | Planned |
| Multi-omic integration & biomarker modelling | MOFA-style factor models; supervised biomarker models with nested cross-validation | Scientist-led |
Specialist modules
Measurable-residual-disease analysis from NGS with an explicit limit of detection on every report. Research-grade; never a clinical result.
Methods
Error-corrected deep sequencing (UMI/duplex); variant tracking across timepoints; IG/TCR clonotype tracking; low-VAF calling; sensitivity and limit of detection reported per assay and sample
Clonal architecture and how it changes under treatment, from bulk VAF or single-cell DNA.
Methods
Bulk VAF and single-cell DNA (Tapestri) clone reconstruction; phylogenetic trees; timepoint dynamics; therapy-pressure analysis
CH calling, VAF trajectories and risk annotation from panels, WES or WGS, in any cohort where CH is a covariate or an endpoint.
Methods
CH variant calling; VAF trajectories; annotation against gnomAD, OncoKB, COSMIC; TP53 allelic state
Linking genotype, transcriptome and surface phenotype across modalities measured on the same individual.
Methods
scRNA + scDNA + CITE-seq + ATAC from one individual; genotype-to-phenotype linking of clones; MOFA-style factor models
Every pipeline ships with
A versioned container (Docker/Singularity); a Nextflow or Python runner; the QC gates (sample QC, pseudoreplication, batch–outcome confounding, multiple testing, power, missing controls); a provenance record per run; figures, tables and public-repository submission support.
Research use only. Not for use in diagnostic procedures. BioMedsAI is not a CLIA-certified laboratory and does not perform clinical testing. BioMedsAI is not a notified body and holds no accreditation for conformity assessment. Evaluations are independent scientific opinions, not regulatory determinations. Sequencing is performed by qualified partner laboratories under their own accreditations.
Thirty minutes with a scientist on your data and your question. No data moves before a written, signed scope.