Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output

Eval-driven skill tuning. Given a task and an LLM-judge rubric, iteratively rewrites a SKILL.md until a downstream executor agent performs well against the judge. Low-code: all evaluation is LLM-as-judge, not deterministic Python.

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Methylation cycle analysis — enzymatic activity profiles, Net Methylation Capacity, BH4 axis estimates, compound heterozygosity detection from SNP genotype data.

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.

Cell segmentation in fluorescence microscopy images. Supports Cellpose/cpsam (Cellpose 4.0) with additional backends planned. Produces segmentation masks, per-cell morphology metrics (area, diameter, centroid, eccentricity), overlay figures, and a report.md.

Genome, transcriptome, and protein completeness assessment via BUSCO v6. Agentic lineage routing from organism description, all three BUSCO modes, auto-lineage support, and full demo mode without the BUSCO binary.

Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.

Detect Neanderthal and Denisovan introgression segments from modern human genomes

Infers genetic super-population ancestry from a 23andMe/AncestryDNA file and computes ancestry-stratified odds ratios with an exploratory Ancestry Elevation Score (AES) showing where ancestry-specific GWAS effect sizes diverge from European reference estimates.

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.

Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

Create a reusable SkillPack from a successful completed task. Use when the user wants to convert a one-off research, coding, analysis, or content workflow into a distributable local SkillPack with `skillpack.json`, local skills under `skills/`, starter prompts, start scripts, and an optional zip package.

Design, improve, and evaluate reusable agent skills with high-quality SKILL.md files, precise trigger descriptions, progressive disclosure, and testable behavior. This skill should be used when users ask to create a new skill, rewrite or review an existing skill, audit a skill collection such as `config/source/skills` for redundancy or overlap, improve skill trigger quality, organize skill references, or evaluate whether a skill should trigger and behave correctly.

Use when running or scheduling periodic repository review cycles that must dispatch the correct reviewer, aggregate findings, and escalate outcomes into reports, issues, or corrective PRs across API contracts, documentation freshness, code quality, and CloudBase skill quality.

Periodically analyze open pull requests for CI failures, code review feedback, and quality issues, then fix them in batch. Use this skill when the user asks to check PR status, triage CI failures, fix review comments, analyze open PRs, or run a scheduled PR health check across the repository.

Spec and no-spec planning workflows derived from local slash commands (requirements, design, tasks).

Triage, repair, and close MCP attribution issues from the local report API with evidence-driven decisions and isolated Worktrunk worktrees. Use this skill when Codex needs to process `tool` attribution issues and skills-related attribution issues, inspect related runs, decide whether the issue is actionable in `mcp/src` or `config/source/skills`, update attribution fields as `owner=codex`, and then complete the fix loop through GitHub issue tracking, worktree-based code changes, PR submission, and follow-up iteration when the problem is repairable.

Analyze, standardize, validate, and sync locally maintained skills into agent skill directories with a `skills` CLI-aligned workflow. Use this skill when Codex needs to turn ad-hoc prompt or rules folders into reusable `SKILL.md`-based skills, install or sync one or more local skills from `./skills` into Claude, Cursor, CodeBuddy, Codex, or similar agent directories, or manage local skill path mappings and symlink or copy installation behavior.