Dados e Análise

Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking. For GWAS use gwas-database; for clinical pathogenicity use clinvar-database.

Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.

Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.

When the user wants to add or optimize Open Graph metadata for social sharing. Also use when the user mentions "Open Graph," "og:tags," "og:title," "og:image," "og:description," "Facebook preview," "LinkedIn preview," or "social share preview." For X (Twitter) link previews, use twitter-cards. For SERP title/description, use title-tag and meta-description.

Comprehensive FastAPI development skill covering REST API creation, routing, request/response handling, validation, authentication, database integration, middleware, and deployment. Use when working with FastAPI projects, building APIs, implementing CRUD operations, setting up authentication/authorization, integrating databases (SQL/NoSQL), adding middleware, handling WebSockets, or deploying Fast

Add comprehensive debugging and observability tooling for backend storage layers (PostgreSQL, ChromaDB) and startup metrics. Includes storage drift detection, raw data inspection endpoints, and a Next.js admin dashboard.

TAM/SAM/SOM calculator with deep market research. Produces comprehensive market-sizing.md with top-down and bottom-up estimates, methodology, data sources, assumptions, sensitivity ranges, growth projections, competitive landscape, and Mermaid visualizations. Use when user needs market size estimates, addressable market analysis, go-to-market sizing, investor-ready market analysis, or business pla

Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.

Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic fe

AI-enhanced copy number variation calling and analysis from sequencing data for cancer genomics, constitutional CNV detection, and chromosomal aberration characterization.

End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.