Biological Data Analysis
From raw files to publication-ready figures.
You send us your data. We send back answers. That is the simple version. I build end-to-end analysis pipelines for scRNA-seq, bulk transcriptomics, flow cytometry, and imaging, and deliver documented, reproducible code alongside clear results you can actually use.
Single-Cell RNA-seq (scRNA-seq)
I take your FASTQ files or Cell Ranger outputs through QC, ambient RNA correction (SoupX/CellBender), normalization, batch integration, clustering, cell type annotation, and differential expression. I use pseudobulk methods for between-condition comparisons so your statistics hold up under reviewer scrutiny. You get a fully documented Seurat or Scanpy pipeline, publication-ready figures, and a plain-English summary of what the data shows.
Bulk Transcriptomics
Differential expression (DESeq2, limma), pathway enrichment (GSEA, over-representation analysis), and immune deconvolution (CIBERSORTx). I also integrate across omic layers when you have matched RNA and protein data. Deliverables include publication-ready volcano plots, heatmaps, and PCA visualizations.
Flow Cytometry
I replace manual gating with reproducible, scripted analysis. High-dimensional reduction (UMAP, tSNE), automated clustering (FlowSOM, PhenoGraph), and statistical comparisons across conditions. If your panel has 15 or more markers, I can find populations you would miss with traditional biaxial gating.
Microscopy & Imaging
Automated quantification of IHC and IF staining intensity across hundreds of tissue sections. I build ImageJ and Python pipelines that eliminate inter-rater variability and cut analysis time from days to hours. For spatial transcriptomics (Visium, MERFISH), I handle the full analysis from spot deconvolution to spatial differential expression.
What You Get
- End-to-end pipelines customized to your experimental setup and data structure
- Publication-ready figures (UMAP, volcano plots, heatmaps, gating overlays)
- Documented, reproducible code in R or Python (no black boxes)
- Written interpretation of results: what the data shows and what it means biologically
- Consultation on design, reproducibility, and downstream analysis strategy
We do not just run the tools. We help you ask the right questions, avoid common analytical pitfalls, and move confidently from raw data to results that hold up under review.
Related Services
Have a dataset sitting in a folder? Let's talk about what it would take to turn it into a figure.
Book a Free 30-Minute Call