Services & how we work

Every engagement includes the read on what it means.

Each service below is a complete engagement, scoped to your biological question and written up as an interpretation: what stands out for your system and what is worth testing next, not just a folder of figures. Fixed scope and turnaround agreed up front; a quote comes back within 2 business days.

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Expert review

A second opinion on results you already have. Not a re-run, a read: do the conclusions hold?

Typical scope
1 dataset / 1 contrast
Turnaround
2 business days
  • • A plain read of what the results mean for your biology
  • • The two or three things worth digging into next
3 more deliverables
  • • A check of your thresholds, outliers and normalisation choices, and what I would change and why
  • • A short methods paragraph ready for a paper or grant
  • • Credited against the project fee if it becomes a full analysis
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RNA-seq (bulk)

Which genes and pathways actually move, and what that says about your system.

Typical scope
24 samples
Turnaround
7 business days
  • • A written read of the differential expression: what the signal means for your biology
  • • Pathway and TF-activity interpretation, not just a GSEA table
3 more deliverables
  • • DESeq2 differential expression with shrinkage; PCA, volcano, heatmap
  • • GSEA (GO, KEGG, Reactome) + TF activity (DoRothEA / decoupleR)
  • • Adapter trimming, splice-aware alignment and gene quantification (fastp, MultiQC)
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scRNA-seq

Which cell populations change between conditions, and the programs driving them.

Typical scope
16 libraries
Turnaround
10 business days
  • • A written read of which populations shift and what that means
  • • Cross-condition differential expression interpreted at the program level
3 more deliverables
  • • UMAP / Leiden clustering + automated cell-type annotation
  • • Marker genes per cluster; QC, doublet removal, normalization
  • • AnnData object (.h5ad) included
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Proteomics

Which proteins and pathways shift at the protein level, read against your biology.

Typical scope
24 samples
Turnaround
7 business days
  • • A written read of the differential abundance and its biological meaning
  • • Pathway interpretation (GO, KEGG, Reactome)
2 more deliverables
  • • MSstats / limma differential abundance; PCA, volcano, heatmap
  • • Search-engine ingest (MaxQuant, DIA-NN, FragPipe); LFQ / TMT / SILAC
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Phosphoproteomics

Which signaling pathways and kinases are active, not just which sites change.

Typical scope
24 samples
Turnaround
10 business days
  • • A written read of the active signaling, at the kinase and pathway level
  • • Kinase activity inference (KSEA / decoupleR) + kinase–substrate networks
2 more deliverables
  • • Phosphosite-level quantification with class-I localization
  • • All proteomics deliverables
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ChIP-seq

Where a factor binds across the genome, what it regulates, and how that changes.

Typical scope
24 samples
Turnaround
7 business days
  • • A written read of the binding landscape and its regulatory meaning
  • • Peak annotation + motif interpretation (ChIPseeker, HOMER)
2 more deliverables
  • • Peak calling (MACS3, narrow or broad); differential binding (DiffBind)
  • • Alignment (Bowtie2); BED / narrowPeak files included
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ATAC-seq

Where chromatin opens and closes, and which regulators sit behind the change.

Typical scope
24 samples
Turnaround
7 business days
  • • A written read of the accessibility changes and the regulators implicated
  • • Optional TF footprinting interpretation (TOBIAS)
2 more deliverables
  • • Accessible-region calling (MACS3 BAMPE); differential accessibility (DiffBind)
  • • ENCODE QC (TSS enrichment, fragment size); nucleosome positioning
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DNA methylation

Where the methylome shifts and how to read the direction correctly.

Typical scope
24 samples
Turnaround
10 business days
  • • A written read of the differentially methylated regions and their meaning
  • • Genomic-context annotation so direction is interpreted correctly
2 more deliverables
  • • Per-CpG calls + DMR detection (methylKit; dmrseq / DSS on request)
  • • Bisulfite/enzymatic alignment (Bismark) with conversion-efficiency QC
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Multi-omics integration

Combine two or more omics layers into one integrated story: MOFA2 factor analysis, patient-specific regulatory networks, and cross-omics pathway convergence, interpreted as a single biological narrative rather than parallel reports.

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Options & add-ons

  • •Rush delivery when you are working against a deadline
  • •Larger studies, extra samples, unusual reference genomes
  • •Follow-up re-analysis and additional contrasts
  • •Ongoing analysis capacity on retainer, after a first project

15% academic discount for requests from .edu / .ac.* institutional emails.

For academic labs

Writing or resubmitting a grant?

We strengthen the proposal with real preliminary data from public sources at no cost, and write the computational arm reviewers now expect. The downstream analysis of your own data is scoped into the budget and run only if the grant is funded, paid from grant funds. Zero risk to you, and no cost until it wins.

Ask about grant support

Custom & enterprise

Outside the standard scope?

Studies above the typical scope, white-label work for CROs, ongoing analysis retainers, novel omics types (spatial, Hi-C, long-read), or unusual reference genomes are all quotable. Email with the details, quote back within 2 business days.

Discuss a custom engagement

What you get, every analysis

Payment terms and a fixed quote are agreed before any work begins. EUR by default; USD invoicing available on request.