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pgraber/README.md

Philipp Graber

Google Scholar ORCID LinkedIn Email

Computational biologist with a wet-lab background, working on paediatric brain cancer.

🔬 Wet lab · 3D tumour models · high-throughput drug screening · imaging
🧬 Computational · single-cell, bulk & small RNA-seq · long-read · drug-response & image analysis
⚙️ Engineering & AI · reproducible, containerised Nextflow pipelines · lab tools (bioprint-tracker) · agentic AI for research (agentic-research-loop)

🛠️ What I work with

R Python Seurat Nextflow Docker Singularity Quarto Git

Popular repositories Loading

  1. pgraber.github.io pgraber.github.io Public

    JavaScript

  2. matrisome-analysis matrisome-analysis Public

    Snakemake workflow for DESeq2 differential expression, functional enrichment and matrisome annotation of paediatric tumour RNA-seq against normal brain.

    R

  3. agentic-research-loop agentic-research-loop Public

    A rigour-first, human-in-the-loop research assistant built as Claude Code skills: pre-registered QC, continuous validation, and a full decision record.

    Python

  4. pgraber pgraber Public

  5. bioprint-tracker bioprint-tracker Public

    eLabNext (SciSure) browser add-on that registers RASTRUM/Allegro bioprint runs as barcoded Inventory records.

    JavaScript

  6. isoform-methods isoform-methods Public

    Reusable, unit-tested R methods for isoform-level single-cell RNA-seq: fractional isoform-to-gene collapse, isoform switching and deltaPI, effect sizes.

    R