Explore AI Agent Skills & Claude Prompts

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ MedToolkit tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis, GO term enrichment, KEGG pathway analysis, GSEA, over-representation analysis, functional annotation, or gene set analysis.

single-cell

Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering, differential expression (Wilcoxon, t-test, DESeq2), cell type annotation, per-cell-type statistical analysis, gene-expression correlation, batch correction (Harmony), trajectory inference, and cell-cell communication analysis. NEW: Analyzes ligand-receptor interactions between cell types using OmniPath (CellPhoneDB, CellChatDB), scores communication strength, identifies signaling cascades, and handles multi-subunit receptor complexes. Integrates with MedToolkit gene annotation tools (HPA, Ensembl, MyGene, UniProt) and enrichment tools (gseapy, PANTHER, STRING). Supports h5ad, 10X, CSV/TSV count matrices, and pre-annotated datasets. Use when analyzing single-cell RNA-seq data, studying cell-cell interactions, performing cell type differential expression, computing gene-expression correlations by cell type, analyzing tumor-immune communication,

pharmacogenomics-agent

AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.

molecular-glue-discovery-agent

AI-powered molecular glue discovery for targeted protein degradation, enabling neo-substrate recruitment and undruggable target degradation through E3 ligase interface modulation.

epigenomics

Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus MedToolkit annotation tools (Ensembl, ENCODE, SCREEN, JASPAR, ReMap, RegulomeDB, ChIPAtlas). Supports BED, BigWig, methylation beta-value matrices, Illumina manifest files, and multi-sample clinical data. Use when processing methylation data, ChIP-seq peaks, ATAC-seq signals, or answering questions about CpG sites, differential methylation, chromatin accessibility, histone marks, or epigenomic statistics.

cancer-variant-interpretation

Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs multi-database analysis covering clinical evidence (CIViC), mutation prevalence (cBioPortal), therapeutic associations (OpenTargets, ChEMBL, FDA), resistance mechanisms, clinical trials, prognostic impact, and pathway context. Generates an evidence-graded markdown report with actionable recommendations for precision oncology. Use when oncologists, molecular tumor boards, or researchers ask about treatment options for specific cancer mutations, resistance mechanisms, or clinical trial matching.

clinical-text-summarization

Summarize long clinical and biomedical text discharge summaries, progress-note bundles, radiology/pathology reports, and literature using extractive and abstractive methods. Covers transformer summarizers (BART/PEGASUS/T5, clinical/long-document variants), chunking for long inputs, and faithfulness/hallucination checking against the source. Use to produce a concise problem-oriented summary, a "one-liner" hospital course, or a literature digest while guarding against fabricated facts.

bio-variant-calling-filtering-best-practices

Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.

tpd-ternary-complex-agent

AI-powered ternary complex prediction for targeted protein degradation, modeling POI-degrader-E3 ligase assemblies to optimize PROTAC and molecular glue efficacy.

expression-data-retrieval

Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.

healthcare-predictive-modeling

Build, tune, and validate supervised predictive models on healthcare data risk of readmission, cost, disease onset, no-show, denial. Emphasizes ML fundamentals done right train/validation/test and cross-validation design, the bias-variance tradeoff, regularization (L1/L2/early stopping), loss-function choice, class imbalance, probability calibration, and leakage-safe, point-in-time feature engineering. Covers scikit-learn, XGBoost/LightGBM, and PyTorch/TensorFlow. Use to develop a robust, well-evaluated clinical or operational predictive model.

jungian-psychologist

Expert in Jungian analytical psychology, depth psychology, shadow work, archetypal analysis, dream interpretation, active imagination, addiction/recovery through Jungian lens, and the individuation process - grounded in primary sources and clinical frameworks. Activate on 'Jung', 'Jungian', 'shadow work', 'archetypes', 'dream interpretation', 'active imagination', 'individuation', 'anima', 'animus', 'collective unconscious', 'addiction', 'recovery', 'spiritus contra spiritum'. NOT for therapy or diagnosis (only licensed analysts diagnose), active psychosis, severe dissociation, or replacing the relational container of actual Jungian analysis.