§ 01 · Practice
Analysis you can defend in a review.
We take raw sequencing, mass-spec or array data through QC, processing, statistics and interpretation. Every result comes with the methods, the code and the environment needed to reproduce it.
§ 01.1 / Scope
Capabilities.
Genomics
Germline and somatic variant calling, structural variants, CNVs, annotation and prioritisation. Short-read and long-read (ONT, PacBio).
Transcriptomics
Bulk RNA-seq differential expression, splicing and fusion detection. Single-cell and spatial: clustering, annotation, trajectories, cell–cell communication.
Epigenomics
ATAC-seq, ChIP-seq and CUT&Tag peak calling, differential accessibility, motif analysis. Bisulfite and nanopore methylation.
Proteomics & metabolomics
Label-free and TMT quantification, imputation, differential abundance, pathway enrichment.
Microbiome & metagenomics
Taxonomic profiling, assembly and binning, functional annotation, AMR gene detection, diversity statistics.
Multi-omics integration
Factor models, network integration and joint embeddings that connect layers instead of stapling results together.
§ 01.2 / Output
Deliverables.
- —Analysis-ready matrices, variant tables and annotated objects
- —A written report with methods you can paste into a manuscript
- —Publication-quality static figures and interactive views
- —Reproducible notebooks with pinned environments
Tools & Standards.
nf-core and community standards where they exist, custom software where they do not.
- GATK
- DeepVariant
- STAR
- Salmon
- DESeq2
- edgeR
- Seurat
- Scanpy
- Cell Ranger
- MACS3
- Bismark
- Kraken2
- MetaPhlAn
- MaxQuant
- MOFA+
§ 01.3 / Questions
Frequently asked questions.
- Do you work with data from any sequencing platform?
- Yes. Illumina, Element, Oxford Nanopore, PacBio, 10x Genomics, Visium and Xenium, plus mass-spec and array data.
- Can you re-analyse a public dataset?
- Yes. We regularly reprocess GEO, SRA, ENA and TCGA data with a consistent pipeline so results are comparable with your own.
- How do you handle sensitive human data?
- Analysis runs on your infrastructure or in an isolated environment you control. We sign a DPA and follow the access rules of your ethics approval.
§ Practice Scoping · 01
Scope a project in omics analysis.
Tell us about your assay types, dataset scale, and timelines. We reply with a preliminary scoping memo within two working days.
Scope Omics Analysis →