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AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.

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.

JetBrains Exposed ORM patterns including DSL queries, DAO pattern, transactions, HikariCP connection pooling, Flyway migrations, and repository pattern.

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

GitHub CLI (gh) comprehensive reference for repositories, issues, pull requests, Actions, projects, releases, gists, codespaces, organizations, extensions, and all GitHub operations from the command line.

Git best practices for commits, branches, pull requests, and collaboration workflows following Conventional Commits and GitFlow patterns

Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.

Calculate portfolio risk metrics including VaR, CVaR, Sharpe, Sortino, and drawdown analysis. Use when measuring portfolio risk, implementing risk limits, or building risk monitoring systems.

Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a give

Use when building UI components. Enforces ShadCN UI patterns, accessibility standards (Radix UI), and TailwindCSS best practices for November 2025.

Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarkers from high-dimensional omics data.

Migrate prompts and code from Claude Sonnet 4.0, Sonnet 4.5, or Opus 4.1 to Opus 4.5. Use when the user wants to update their codebase, prompts, or API calls to use Opus 4.5. Handles model string updates and prompt adjustments for known Opus 4.5 behavioral differences. Does NOT migrate Haiku 4.5.