Results for “complexity”

Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Evaluate code (especially LLM-generated) for structural simplicity using Rich Hickey's "Simple Made Easy" framework. Use this skill whenever reviewing a PR, diff, or code snippet for accidental complexity — particularly when the code was generated by an AI coding assistant and line-by-line review isn't feasible. Also use when the user asks about complecting, simplicity vs. easiness, structural coupling, or concept deduplication. Trigger on phrases like "is this simple", "does this complect", "review for complexity", "structural analysis", or any reference to Hickey, Simple Made Easy, or grey-box review.

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Map a complex topic by placing factors on hexagonal tiles where adjacency signals a claimed relationship. Use when students need to surface hidden connections in a system before analysis or action.

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Enforce complexity and size limits on Swift code with SwiftLint threshold rules — cyclomatic complexity, function/type/file length, parameter count — adopted via a violations baseline so existing code never blocks. Use when agent-written code needs deterministic size constraints.

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Detects time and space complexity hotspots via AST scan. Use when code feels slow, before performance-sensitive merges, or to find O(n²) regressions.

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Evaluate code (especially LLM-generated) for structural simplicity using Rich Hickey's "Simple Made Easy" framework. Use this skill whenever reviewing a PR, diff, or code snippet for accidental complexity — particularly when the code was generated by an AI coding assistant and line-by-line review isn't feasible. Also use when the user asks about complecting, simplicity vs. easiness, structural coupling, or concept deduplication. Trigger on phrases like "is this simple", "does this complect", "review for complexity", "structural analysis", or any reference to Hickey, Simple Made Easy, or grey-box review.

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Use when the user wants to simplify, clean up, refactor, tidy, or refine code — their staged/unstaged git changes or a target file/path. Reduces complexity, flattens nesting, removes redundancy and dead code, scores each change by value (holding low-value churn), then runs tests to prove nothing broke. Invoke on: "simplify", "simplify this", "simplify my code/changes", "clean up", "clean this up", "clean up my changes", "refactor this", "make this cleaner", "tidy this up", "reduce complexity", "flatten this", "remove dead code", "make it more readable", "polish before commit", or "absolute simplify". Acts on your working diff; for repo-wide dead code use absolute-prune; for lint/type debt use absolute-debt.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Map a complex topic by placing factors on hexagonal tiles where adjacency signals a claimed relationship. Use when students need to surface hidden connections in a system before analysis or action.

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Computational thinking as a problem-solving discipline independent of programming languages. Covers the four pillars (decomposition, pattern recognition, abstraction, algorithm design), computational problem-solving methodology (understand, decompose, generalize, formalize, verify), abstraction levels (from hardware through user interface), modeling and simulation, automata and formal languages (DFA, NFA, regular expressions, context-free grammars, Turing machines), computational complexity classes (P, NP, NP-complete, undecidable), and constructionist pedagogy (learning by building, Logo, Scratch, physical computing). Use when approaching unfamiliar problems, teaching problem-solving strategies, analyzing problem complexity, or bridging between domain knowledge and computational solutions.

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Measure whether a change made the tree simpler, on numbers rather than impressions — line counts, branching, coupling, interface width, rule count, standing exemptions and model-visible prose — across one diff or a whole stack of pull requests. Use before claiming a pass reduced complexity, when deciding which pull request in the stack added the machinery, and to read a function's branch count, which no v2 gate reports.

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Managing complexity is software's primary technical imperative - all other goals are secondary

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AI-based complexity assessment for task analysis. Use when determining the appropriate workflow, phases, and validation depth for a task.

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Use when asked to optimize code, make a path faster, make this as fast as possible, reduce allocations, repair a regression, profile a target, grill every inefficiency, or run a subsystem or repo-wide performance campaign against a measured floor; when a performance requirement, slowness report, Core Web Vitals miss, or profiling evidence identifies a bottleneck; or for an "extremely optimize" performance campaign, optimizing suspected hot paths without waiting for benchmarks, or estimating hot and complexity-neutral cold paths while refusing complexity theater. Not for remote, credential, publish, deploy, or irreversible changes.

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Evaluate code (especially LLM-generated) for structural simplicity using Rich Hickey's "Simple Made Easy" framework. Use this skill whenever reviewing a PR, diff, or code snippet for accidental complexity — particularly when the code was generated by an AI coding assistant and line-by-line review isn't feasible. Also use when the user asks about complecting, simplicity vs. easiness, structural coupling, or concept deduplication. Trigger on phrases like "is this simple", "does this complect", "review for complexity", "structural analysis", or any reference to Hickey, Simple Made Easy, or grey-box review.

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Evaluate code (especially LLM-generated) for structural simplicity using Rich Hickey's "Simple Made Easy" framework. Use this skill whenever reviewing a PR, diff, or code snippet for accidental complexity — particularly when the code was generated by an AI coding assistant and line-by-line review isn't feasible. Also use when the user asks about complecting, simplicity vs. easiness, structural coupling, or concept deduplication. Trigger on phrases like "is this simple", "does this complect", "review for complexity", "structural analysis", or any reference to Hickey, Simple Made Easy, or grey-box review.

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Estimate the full development cost of an existing codebase from lines of code, architectural complexity, and team-composition overhead. Use for 'how much would this cost to build', 'what did this codebase cost', development-cost or build-cost estimates, calendar-time estimates, and Claude/AI ROI on a delivered codebase. Estimates by measured LOC and complexity, not by ticket volume.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Analyzes ticket complexity and maps dependencies against an existing codebase before sprint planning. Triggers on 'how complex is this ticket', 'what should we work on first', 'can we fit this in the sprint', 'tech review before planning', 'plan the sprint'. NOT for writing implementation plans (see mk:plan-creator); NOT for scope/ambition review (see mk:plan-ceo-review).

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Detects task agent and complexity tier at Phase 0 orient. Invoked first in every workflow. Provider adapters select any model/runtime policy. NOT for runtime agent routing inside a single skill (see orchestration-rules.md).

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Expert-level algorithms and complexity theory covering sorting, searching, graph algorithms, dynamic programming, greedy algorithms, NP-completeness, and algorithm design paradigms.

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Use when working code feels heavier than it needs to be — deeply nested logic, long functions, unclear names, duplication after a merge, or a review that flagged complexity. Reduces complexity while preserving behavior exactly. Not for code you do not yet understand, or code you are about to rewrite.

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Mitigate incidental code complexity when control flow is tangled, nesting is deep, names are hard to parse, or reasoning requires cross-file hops. Use when a review stalls on readability, you need an analysis-first refactor plan before edits, or you want essential-vs-incidental verdicts, ranked simplification steps, a small structural sketch, and a TRACE assessment (analysis-only; no edits).

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Use when the operator says "run distillation" or "refresh complexity corpus", or a distillation pass is due.

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