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Analyze text readability with Flesch-Kincaid, Gunning Fog, SMOG, and other metrics. Returns objective scores with interpretation and recommendations.

Expert patterns for Segment Customer Data Platform including Analytics.js, server-side tracking, tracking plans with Protocols, identity resolution, destinations configuration, and data governance best practices. Use when: segment, analytics.js, customer data platform, cdp, tracking plan.

Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence, and predict epitope specificity. Integrate with single-cell data for clonotype-phenotype associations. Use for adaptive immune response profiling, cancer immunotherapy research, vaccine response ass

AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks clinical trials from ClinicalTrials.gov using multi-dimensional matching across molecular eligibility, clinical criteria, drug-biomarker alignment, evidence strength, and geographic feasibility. Produces a quantitative Trial

Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.

Master ShellCheck static analysis configuration and usage for shell script quality. Use when setting up linting infrastructure, fixing code issues, or ensuring script portability.

Software architecture and UI/UX principles for building genuinely new solutions, not derivative work. Use when designing features, architecting software, brainstorming apps, reviewing designs, or during strategy discussions. Focuses on first-principles thinking, simplicity where it matters, and creating rather than commenting.

Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions, and drug targets. Perform sgRNA count processing, gene-level scoring (MAGeCK, BAGEL), quality control, pathway enrichment, and drug target prioritization. Use for CRISPR screen analysis, gene essentia

Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling i

Create and manage Claude Code plugins with proper structure, manifests, and marketplace integration. Use when creating plugins for a marketplace, adding plugin components (commands, agents, hooks), bumping plugin versions, or working with plugin.json/marketplace.json manifests.

Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs. Use when creating circular genome visualizations.

PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.