All skills
PrimeKG Precision Medicine Knowledge Graph
Query the PrimeKG biomedical knowledge graph — genes, drugs, diseases, phenotypes — straight from Claude Code.
PyDESeq2 Differential Expression
An end-to-end guide for bulk RNA-seq differential expression with PyDESeq2 — formulaic designs, Wald tests, FDR correction, LFC shrinkage, and plots.
Rowan Molecular Modeling Workflows
A skill that drives Rowan's cloud chemistry API to run pKa prediction, docking, conformer/tautomer searches, and protein–ligand cofolding from code.
PennyLane Quantum ML
A skill that guides building, training, and deploying differentiable quantum circuits with PennyLane.
RDKit Cheminformatics Toolkit
A guide for doing molecular work with RDKit — parsing SMILES/SDF, descriptors, fingerprints, substructure search, reactions, and 2D/3D coordinates.
TorchDrug Workflow Assistant
Writes and debugs TorchDrug 0.2.1 code for molecular property prediction, generation, retrosynthesis, protein encoders, and knowledge graph reasoning.
PathML Computational Pathology Workflow
A research-only skill for using PathML 3.0.5 to tile slides, build preprocessing/QC pipelines, quantify multiplex images, construct spatial graphs, and plan bounded local inference.
ETE Toolkit 4 Phylogenetic Tree Analysis
Guides Claude to analyze, edit, compare, annotate, and visualize existing phylogenetic trees with ETE 4.4.0.
HypoGeniC Run Planner & Auditor
Plans, audits, and cost-bounds ChicagoHAI HypoGeniC/HypoRefine hypothesis-generation runs entirely locally before any LLM call.
PufferLib RL Guide
Version-aware guidance for PufferLib RL work — environment adaptation, vectorization, PuffeRL training, and safe checkpoint review across the 3.0.0 release and 4.0 source line.
Medchem Compound Filtering
Triage compound libraries with drug-likeness rules (Lipinski, Veber, CNS), PAINS/NIBR structural alerts, complexity metrics, and the medchem query language.
matchms Mass Spectra Toolkit
A skill for cleaning, filtering, comparing, and library-searching MS/MS spectra with the current matchms 0.33.1 API.
Neuropixels Analysis
An end-to-end SpikeInterface workflow for Neuropixels recordings: loading, preprocessing, drift correction, spike sorting, quality metrics, and unit curation.
Pi Agent Helper
A routing-style skill for installing, configuring, and building on Pi, the minimal terminal coding harness.
Paperclip Biomedical Literature CLI
Drives the GXL Paperclip CLI to search and read ~11M full-text biomedical papers, FDA/PMDA/EMA filings, clinical trials and protein records, with line-pinned citations.
DNAnexus Integration
A skill for building, running and monitoring reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets and workflow importers.
Ginkgo Cloud Lab Protocol Guide
A reference skill for picking, configuring and ordering automated wet-lab protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio).
Geniml Genomic-Interval ML Auditor
A Geniml-focused skill that validates BED/universe contracts and plans Region2Vec, scEmbed, and consensus-universe runs with safety and compatibility checks.