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Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) where the contact background is peak-anchored and coverage-biased, so generic Hi-C loop callers (cooltools dots, Juicer HiCCUPS) use the wrong null. Covers FitHiChIP (config-driven coverage+distance-decay spline regression, peak-to-peak vs peak-to-all foreground, loose vs stringent background, coverage vs ICE bias), MAPS (positive Poisson regression on bias factors for PLAC-seq/HiChIP), hichipper (restriction-site-distance bias model + library QC), CHiCAGO (Delaporte two-component Brownian+technical background for asymmetric bait x other-end Capture Hi-C), the with/without separate-ChIP anchor decision, and differential loops via diffloop. Use when calling loops from HiChIP/PLAC-seq/Capture Hi-C, choosing FitHiChIP/MAPS/CHiCAGO, picking peak-to-all vs peak-to-peak, setting the loop FDR, supplying ChIP peaks as anchors, QCing a HiChIP library, or comparing loops between conditions.

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Find repeated engineering tasks and turn them into agent workflows with clear checks, stopping rules, and approval boundaries. Compare published workflows, adapt suitable examples, or review existing ones for weak verification and uncontrolled repetition.

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• Find recurring tasks in code and conversation history
• Compare and adapt published agent workflows
• Review workflows for weak checks and missing stop rules

Load project rules before an agent starts work, then apply restrictions to file edits, tests, pushes, and merges. Check pause settings and identify actions that require human approval.

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• Applying project rules before automated work
• Checking protected paths before editing
• Reviewing push and merge conditions

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Start a safe, governed autonomous loop from a plain-language goal. Use when the user says /coco-loop, "run an autonomous loop", "keep my build green for N hours", "work on X autonomously for a while", or wants a bounded self-improving loop that proposes fixes and never commits on its own. Turns a vague goal into a readable charter the user confirms, then arms and runs the loop propose-only under the coco-loops governance framework.

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Design and review autonomous or semi-autonomous agent loops — systems where an agent prompts itself, runs on a schedule or event, and iterates toward a goal without a human at the keyboard. Use this whenever the user wants to build, design, harden, or audit any kind of self-running agent, agentic workflow, control loop, background worker, cron/heartbeat/webhook-driven agent, "Ralph loop", auto-PR-fixer, monitoring agent, or any long-running task that should keep going on its own until done. Trigger this even when the user says "agentic workflow", "automation that runs itself", "an agent that keeps trying until X", or "make my agent stop running away / burning tokens" without using the word "loop". Also use it to review an existing loop's stopping conditions, guardrails, verification, and escalation paths.

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反復レビュー・ループ(codex-review-loop・fable-review-loop・opus-review-loop)が共有する判断ロジックの正本。起動可否ゲート・レビュアーの正体に依存しない大前提・常設観点・レビュー依頼に含める内容と含めてはならない内容・照合仕分け・終了判定・報告を定義する。内部専用でユーザーが直接使うものではない。

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Run Ruflo background workers on a recurring schedule within a Claude Code session. Choose tasks such as security analysis, documentation, or test coverage analysis, check their status, and stop the loop after repeated reports of no new work.

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• Run recurring security analysis
• Periodically check test coverage gaps
• Repeat code analysis and documentation tasks

Design recurring marketing workflows for SEO checks, ad reviews, and churn monitoring. Define when an agent checks, when it acts, what requires human approval, and when it stops, using reusable workflow templates.

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• Set up a weekly SEO review
• Schedule recurring ad fatigue checks
• Monitor customer churn signals

Coordinate AI research from literature review and hypothesis testing to findings and paper drafts. The skill alternates focused experiments with broader reflection, maintains project records, and directs specialized skills to carry out research tasks.

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• Turning a research question into testable hypotheses
• Managing repeated experiments across multiple hypotheses
• Resuming research from recorded findings and project state

Check estimated token usage against daily limits before and after each automated loop run. Switch to reporting only, exit early when required, and record run outcomes so repeated agent work stays within configured limits.

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• Checking daily token usage before a run
• Switching to reporting only near budget limits
• Exiting early when there is no actionable work

Drafts a token budget extension request when an autonomous loop approaches its daily limit and high priority work remains. Uses logged results and remaining issues to justify the request, then pauses until a human increases the budget.

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• Requesting extra budget for remaining critical work
• Summarizing daily token spending and successful actions
• Preparing a budget request for a human maintainer

Optional maintainer workflow for the approval, merge-readiness, or authorized self-merge decision on a LoopX pull request. Requires the exact-head review evidence from `loopx pr-review`. Review depth, verdicts, review comments, and the published review format belong to loopx-pr-review.

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Use for `/loopx-pr-review` or evidence-backed PR queue review. Run `loopx pr-review` first, execute the capability-owned review plan for each selected exact head, then publish full bilingual PR reviews (complete Chinese five-block review plus one concise English verdict) that match the verified findings. Use `loopx-pr-merge` for approval or merge actions.

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Compatibility alias for Loopy. Use only when an existing installation or older instruction explicitly invokes loop-library; use Loopy for new installations and requests. Provides the same discovery, recommendation, audit, repair, adaptation, guided crafting, bounded execution, run debrief, project loop saving, and publication-preparation workflows.

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Spin up a new loop (domain) in a file-based knowledge base — bootstrap the substrate if it's missing, gather the loop's charter, scaffold domains/<loop>/README.md, then do ONE real test run and record it in the loop's Timeline and LOG.md. Use when the user says "set up a new loop", "create a domain", "start a new beat/workstream", or names a recurring job they want the agent to own.

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When the user wants to set up a recurring, self-running marketing workflow — a repeatable loop an AI agent runs on a cadence (weekly, daily, on a trigger) rather than a one-off task. Also use when the user mentions 'marketing loop,' 'recurring marketing workflow,' 'automate my marketing,' 'marketing on autopilot,' 'weekly marketing review,' 'ad fatigue check,' 'content refresh loop,' 'churn watch,' 'ranking drop alert,' 'always-on marketing,' 'marketing automation workflow,' or 'run this every week.' Use this to pick, adapt, and schedule an ongoing marketing loop that orchestrates the other marketing skills. For one-off marketing ideas, see marketing-ideas. For the experimentation loop specifically, see ab-testing.

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Turn a one-line description of a repetitive task into a reusable, self-guarding slash command. loop-forge diagnoses the task into one of 5 loop shapes (Batch / Pipeline / Refine / Watch / Explore), interviews for the blanks, and auto-injects two safety devices the user didn't know they needed — an independent verifier (maker ≠ checker) and a hardstop (a budget/count/cooldown ceiling) — then previews the result and stamps it as a `/command` they can run forever. Use when the user says "/loop", "/loop-forge", "/make-it-loop", "automate this", "make this repeatable", "turn this into a command", "do this for all 100 items", "do X every time Y happens", "generate several and pick the best", or otherwise wants to capture a recurring task as a reusable slash command instead of re-typing the prompt by hand. Works in any language: it interviews the user and writes the stamped command in the user's own language. Non-goal — it does not schedule unattended runs (launchd/cron) or publish externally on its own; it stamps the reusable command and stops there.

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Sets up BMAD Loop Skills module in a project. Use when the user requests to 'install bmad-loop module', 'configure BMAD Loop Skills', or 'setup BMAD Loop Skills'.

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Use when the user asks for Superloopy clone or asks to clone, rebuild, reverse-engineer, replicate, or copy a website or page into a Superloopy-governed implementation. Triggers on "loopy clone", target URLs plus requests such as "clone this site", "rebuild this page", "make a copy of this website", "pixel-perfect clone", or "AI website clone". Requires browser automation and records component specs, assets, implementation, build output, and visual QA as Superloopy evidence.

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Inspect and explain bmad-loop run artifacts under `.bmad-loop/runs/`. Use for live health checks ("is it stuck?", "is the loop alive?", "what is the agent doing?") and post-run forensics ("what happened?", "why did story X fail?", "where did the tokens go?"). Also triggers on "monitor/check/summarize the loop", "why did the run pause?", Vietnamese "theo dõi bmad loop", "phân tích run", "đọc log của run", and equivalent requests in other languages. Use only for bmad-loop's own run artifacts, not application runtime logs or CI-provider build logs.

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Select a `delaySeconds` value when scheduling a loop wakeup via the `ScheduleWakeup` tool or the `/loop` slash command. Covers the three-tier cache-aware decision (cache-warm under 5 minutes, cache-miss 5 minutes to 1 hour, idle default 20 to 30 minutes), the 300-second anti-pattern, the [60, 3600] runtime clamp, the minute-boundary rounding quirk, and writing a telemetry-worthy `reason` field. Use when designing an autonomous loop, when a heartbeat cadence is being planned, when polling cadence is being tuned, or when post-hoc review of loop costs reveals interval mis-sizing.

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