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Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages i…
Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strat…
Test CLI applications interactively using tmux sessions. Use when testing TUI apps (ratatui dashboard, interactive prompts), verifying CLI command output, testing keyboard navigation, or validating te…
Reviews and suggests improvements for Android/Kotlin code. Used when requesting a code review, Android review, or Kotlin review.
Test and debug Mom Factura Payment API integrations using QA environment and payment simulation. Use when setting up test environments, simulating payment outcomes (success, failure, timeout), debuggi…
This skill should be used when the user asks to "validate Perl script", "check Perl syntax", "verify Perl code", "/perl-validate", or mentions script validation, compile check, security review, or bes…
Implement security best practices for Lindy AI integrations. Use when securing API keys, configuring permissions, or implementing security controls. Trigger with phrases like "lindy security", "secure…
Deletes merged git branches (local and remote) and flags stale unmerged branches for manual review. Use when user mentions "cleanup branches", "delete merged branches", "prune old branches", "remove s…
Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative …
Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detects hub genes and module-trait relationships from bulk …
Plan and evaluate mesh generation for numerical simulations. Use when choosing grid resolution, checking aspect ratios/skewness, estimating mesh quality constraints, or planning adaptive mesh refineme…
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Review and reorganize Claude Code permission settings across all config files (global settings.json, project settings.local.json, dotfiles copies). Identifies redundancy, misplaced permissions, and la…
Validate Python shebangs and PEP 723 inline script metadata. Use when checking if Python files have correct shebangs based on their dependency requirements, when fixing incorrect shebang patterns, or …
Identify and clean up stale git branches locally and on remotes with safe, reversible steps. Use when asked to prune, list, or delete merged/old branches or audit branch hygiene.
Spring Security 7 implementation for Spring Boot 4. Use when configuring authentication, authorization, OAuth2/JWT resource servers, method security, or CORS/CSRF. Covers the mandatory Lambda DSL migr…
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or h…
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection. Use for calibration, uncertainty studies, parameter sweeps, LHS sampling, Sob…
Analyze and optimize Aptos Move contracts for gas efficiency, identifying expensive operations and suggesting optimizations. Triggers on: 'optimize gas', 'reduce gas costs', 'gas analysis', 'make cont…
This skill should be used when the user asks about "POSIX compatibility", "portable shell scripts", "cross-shell compatibility", "bashisms", "shebang selection", or mentions writing scripts that work …
Python coding standards and best practices. Suitable for code generation, code review, and code refactoring scenarios.
Upgrade dependencies for Java/Kotlin (Gradle/Maven) and TypeScript/Node projects with minimal risk: plan the bump, apply changes incrementally, run tests/builds, and document breaking changes. Use whe…
Analyze and consolidate Flyway SQL migrations into clean, domain-grouped CREATE TABLE migrations for pre-production projects. Use when consolidating database migrations, refactoring Flyway schemas, si…