Biological Data Analysis
From raw files to publication-ready figures.
You send me raw data. I 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
I do not just run the tools. I help you ask the right questions, avoid common analytical pitfalls, and move confidently from raw data to results that hold up under review.
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