Validates inputs, generates pacsomatic samplesheets and launch artifacts, then runs or submits nf-core/pacsomatic tumor-normal analyses locally or on HPC schedulers.
Safely read, validate, and export protocols.io data using the current v3/v4 endpoint contracts, with mutations limited to non-executing dry-run plans.
Query the PrimeKG biomedical knowledge graph — genes, drugs, diseases, phenotypes — straight from Claude Code.
An end-to-end guide for bulk RNA-seq differential expression with PyDESeq2 — formulaic designs, Wald tests, FDR correction, LFC shrinkage, and plots.
A skill that drives Rowan's cloud chemistry API to run pKa prediction, docking, conformer/tautomer searches, and protein–ligand cofolding from code.
A skill that guides building, training, and deploying differentiable quantum circuits with PennyLane.
A guide for doing molecular work with RDKit — parsing SMILES/SDF, descriptors, fingerprints, substructure search, reactions, and 2D/3D coordinates.
Writes and debugs TorchDrug 0.2.1 code for molecular property prediction, generation, retrosynthesis, protein encoders, and knowledge graph reasoning.
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.
Guides Claude to analyze, edit, compare, annotate, and visualize existing phylogenetic trees with ETE 4.4.0.
Plans, audits, and cost-bounds ChicagoHAI HypoGeniC/HypoRefine hypothesis-generation runs entirely locally before any LLM call.
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.
Triage compound libraries with drug-likeness rules (Lipinski, Veber, CNS), PAINS/NIBR structural alerts, complexity metrics, and the medchem query language.
A skill for cleaning, filtering, comparing, and library-searching MS/MS spectra with the current matchms 0.33.1 API.
An end-to-end SpikeInterface workflow for Neuropixels recordings: loading, preprocessing, drift correction, spike sorting, quality metrics, and unit curation.
A routing-style skill for installing, configuring, and building on Pi, the minimal terminal coding harness.
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.
A skill for building, running and monitoring reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets and workflow importers.
A reference skill for picking, configuring and ordering automated wet-lab protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio).
A Geniml-focused skill that validates BED/universe contracts and plans Region2Vec, scEmbed, and consensus-universe runs with safety and compatibility checks.