Claude Skills
The open format is called Agent Skills and works in Claude Code, Codex, Cursor and other agents — most people know it as Claude Skills.
Every Agent Skill we could find on GitHub, deduplicated by content. 79 870 files from 1 769 authors, of which 62 217 are unique — the rest is the same skill repackaged into someone else's repository. For each one: what it weighs in tokens, whether it ships runnable scripts, and which MCP servers it needs.
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output
Classify germline variants from VCF/BCF files according to the ACMG/AMP 2015 28-criteria evidence framework and generate clinical-grade interpretation reports with per-variant evidence audit trails and ACMG SF v3.2 secondary findings screening.
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
Deterministic CRISPR screen hit ranking from local guide-level count tables
Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.
>- Full reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D*/F*, R2), linkage disequilibrium (D, D', R², ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA multi-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectrum (sfs, folded and outgroup-unfolded), transition/transversion ratio (tstv), and codon usage bias - RSCU (Sharp & Li 1987) and ENC (Wright 1990) (codon). Accepts FASTA or NEXUS input; outputs DnaSP-compatible TSV and a Markdown report.
Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance
| Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset
Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.
>- Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).
Statistical fine-mapping of GWAS loci using SuSiE, SuSiE-inf, and Approximate Bayes Factors to identify credible sets and posterior inclusion probabilities (PIPs) for causal variant discovery. SuSiE-inf adds an infinitesimal polygenic component for improved calibration at well-powered loci.
Flow.bio API bridge — authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions, and check run status on any Flow instance.
Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
Score genetic compatibility across all male-female pairings in a Genomebook generation
| Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST TSV slice in canonical format.
Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Produces Manhattan plots, QQ plots, clumped lead variants, and structured summary statistics.
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle. '
Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and full sensitivity analysis (Cochran Q, Egger intercept, Steiger, F-statistic, leave-one-out).
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.
>- Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.
Wrapper skill for running nf-core/scrnaseq upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.
Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.
Aggregate public target-level evidence across omics and translational sources for research triage.
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
Compute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.
Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output. Workflow includes preprocessing, imputation, and statistical testing.
Search PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language papers.
Blood RNA-seq expression-outlier detection for rare-disease diagnostics. Cases scored against a control reference panel; outliers ranked and filtered by a haploinsufficient disease-gene panel.
Produce offspring genomes from parent pairs via meiotic recombination, mutation, and clinical evaluation
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
NGS read QC, alignment, and BAM processing pipeline. Wraps FastQC, BWA/Bowtie2/Minimap2, SAMtools, and MultiQC for automated read-to-BAM workflows.
Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json
Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping
Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.
Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns
Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.
Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.
Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.
Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.
> Query the ADReCS (Adverse Drug Reaction Classification System) v3.3 database. Use whenever the user asks about adverse drug reactions, drug safety profiles, ADR classification, ADR severity/frequency, or wants to look up any entity (drug name, BADD Drug ID, DrugBank ID, ATC code, CAS RN, PubChem CID, KEGG ID, ADR term, ADReCS ID, MedDRA code, MeSH ID) in ADReCS.
> Query the WHO ATC/DDD Classification System. Use whenever the user asks about ATC codes, drug classification hierarchy, Defined Daily Doses (DDD), or wants to look up drugs by ATC class or find the ATC code for a drug name.
> Query the BindingDB drug-target binding affinity database. Use whenever the user asks about protein-ligand binding data, affinity measurements (Ki, IC50, Kd, EC50), or wants to look up binding partners for a UniProt ID, PDB ID, or compound SMILES string.
> Query the CADEC (CSIRO Adverse Drug Event Corpus). Use whenever the user asks about adverse drug event mentions in consumer health text, entity annotations from patient forum posts, MedDRA/SNOMED-CT normalised ADR spans, or wants to look up drugs, symptoms, or coded entities in the CADEC corpus.
> Query the ChEBI (Chemical Entities of Biological Interest) database. Use whenever the user asks about small molecule identifiers, chemical ontology roles, molecular formulae, SMILES, InChI, synonyms, or cross-references for biologically relevant chemical compounds via ChEBI.
Claude Skills — questions
Answers built from the skills we actually parsed.