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Generates complete NHANES-style cross-sectional epidemiology + retrospective clinical validation research designs from a user-provided disease and biomarker direction. Always use this skill whenever a user wants to design, plan, or build a population-level biomarker association study using NHANES or similar survey datasets, especially when the article logic includes disease definition, biomarker formula derivation, multivariable logistic regression, restricted cubic spline analysis, subgroup stability testing, and a secondary hospital-based retrospective validation cohort. Covers five study patterns (cross-sectional association, dose-response / RCS, subgroup-stability, NHANES + retrospective validation, preliminary screening-performance) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.

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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.

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Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

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The Power BI report design canon covering design identity, visual hierarchy and the 3-30-300 rule, layout/spacing/alignment, color discipline, chart selection, KPI and card design, tables and matrices, accessibility, and the closing design gate. The shared reference home for report design judgment, routed to by the create-pbi-report, pbir-cli, review-report, modifying-theme-json, and custom-visual skills. Load when committing a design identity or making a design, layout, color, chart-selection, or accessibility decision for a report.

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Arbitrator research tool for investor-State dispute settlement (ISDS). The tool can summarize arbitrators' experience, with deliverables grounded in primary documents; it can also help find arbitrators based on the issues faced in a particular case. Use when the user asks about an arbitrator ("tell me about arbitrator X", "X, Y and Z"), wants help choosing or shortlisting arbitrators for a case, or asks about appointments, dissents, issue track records (e.g. FET, expropriation), challenge risk, double-hatting, or tribunal composition. Profiles are grounded in the UNCTAD ISDS Navigator dataset plus targeted live lookups (ICSID); deep verification retrieves the actual decisions. Sibling of isds-research.

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Expert patterns for RPG/action ability systems including cooldown strategies, combo systems, ability chaining, skill trees with prerequisites, upgrade paths, and resource management. Use when implementing unlockable abilities, character progression, or complex skill systems. Trigger keywords: PlayerAbility, AbilityManager, cooldown, SkillTree, SkillNode, prerequisites, can_use, execute, ComboSystem, ability_chain, global_cooldown, charge_system, upgrade_path.

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Expert patterns for porting desktop games to mobile including touch control schemes (virtual joystick, gesture detection), UI scaling for small screens, performance optimization for mobile GPUs, battery life management, and platform-specific features. Use when creating mobile ports or cross-platform mobile builds. Trigger keywords: TouchScreenButton, virtual_joystick, gesture_detector, InputEventScreenTouch, InputEventScreenDrag, mobile_optimization, battery_saving, adaptive_performance, MOBILE_ENABLED.

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Expert patterns for RPG/action ability systems including cooldown strategies, combo systems, ability chaining, skill trees with prerequisites, upgrade paths, and resource management. Use when implementing unlockable abilities, character progression, or complex skill systems. Trigger keywords: PlayerAbility, AbilityManager, cooldown, SkillTree, SkillNode, prerequisites, can_use, execute, ComboSystem, ability_chain, global_cooldown, charge_system, upgrade_path.

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Expert patterns for porting desktop games to mobile including touch control schemes (virtual joystick, gesture detection), UI scaling for small screens, performance optimization for mobile GPUs, battery life management, and platform-specific features. Use when creating mobile ports or cross-platform mobile builds. Trigger keywords: TouchScreenButton, virtual_joystick, gesture_detector, InputEventScreenTouch, InputEventScreenDrag, mobile_optimization, battery_saving, adaptive_performance, MOBILE_ENABLED.

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This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.

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The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to

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EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. Thi

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This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

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epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

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Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '

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The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and enc

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Manage capa CLI configuration — `capabilities.yaml` / `capabilities.json`, skills, MCP servers, tools, hooks, sub-agents, rules, plugins, AGENTS.md / CLAUDE.md, security options, tool exposure modes, `capa wrap` shadow workspaces, `--passthrough` native writes, registries (including Claude marketplaces), activity traces, and the local Web UI. Use whenever the user edits the capabilities file, runs any `capa` command (init, install, add, wrap, clean, sh, start/stop/restart/status, auth, upgrade, cache, registry), wires up an MCP server, adds a skill from GitHub / GitLab / a registry / a remote URL / a local path, configures secrets via `${VarName}` placeholders, installs lifecycle hooks, defines sub-agents, or troubleshoots a failed install. Use even when the user only names a fragment ("add a skill", "wire up brave search", "wrap cursor", "block this phrase in skills") without saying "capa" — if a `capabilities.yaml` or `capabilities.json` lives at the project root, this is almost certainly the right skill. If the project does NOT yet have a capabilities file, point at the `bootstrap` skill instead.

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Use Biome in .NET repositories that ship Node-based frontend assets and want a fast combined formatter-linter-import organizer for JavaScript, TypeScript, CSS, JSON, GraphQL, or HTML. USE FOR: biome.json or @biomejs/biome setup; fast frontend formatting and linting; replacing overlapping frontend style tools deliberately. DO NOT USE FOR: ESLint-only plugin coverage; runtime site audits such as headers, accessibility, or browser behavior. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Audit iOS and Android mobile applications against OWASP MASVS / MASTG — insecure storage, weak crypto, certificate pinning, deeplinks, IPC, jailbreak/root detection, reverse-engineering resistance. Use when the user mentions 'mobile security,' 'iOS security,' 'Android security,' 'mobile audit,' 'mobile pentest,' 'MASVS,' 'MASTG,' 'certificate pinning,' 'jailbreak detection,' 'root detection,' 'deeplink,' 'URL scheme,' 'app transport security,' 'keychain,' 'keystore,' 'mobile reverse engineering,' or has a mobile app to review.

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