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Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to

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Manage Azure DevOps projects, work items, repos, PRs, pipelines, wikis, test plans, security alerts, variable groups, environments/approvals, branch policies, and attachments. Use when user asks to: manage sprints, create/update work items, list repos, create PRs, run pipelines, search code, manage wiki pages, check security alerts, manage variable groups, approve deployments, or configure branch policies. Covers 13 domains with 99 tools via REST API.

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Apply the changes from all open Renovate bot pull requests of a GitHub repository into the local working tree. Use this skill when asked to apply, merge locally, consolidate, batch, or try out Renovate/dependabot-style dependency update PRs so the combined upgrade can be built and tested in one go. This skill only modifies local files; it never commits, pushes, merges, or closes anything on GitHub.

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Manages stacked PRs and splits multi-part work into reviewable branches with gh-stack. Use for stack creation, viewing, edits, push, submit, sync, rebase, merge, or checkout; when asked to split or isolate work for review; whenever a user mentions a stack, branch layers, dependent PRs, or gh stack; or when a stack is checked out.

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Use when the user asks to audit what's wrong with a project, "make it right", "看看项目出了什么问题", "为什么用户的需求还没上线", "为什么没提交App Store", "为什么没新build", or wants a holistic state-of-the-project check covering unmerged branches, stalled PRs, failed GitHub Actions, stale builds, plan drift (TODOS.md / ROADMAP), unreleased commits, and log errors. Runs read-only investigation, presents a grouped checklist, fixes only after explicit user confirmation. Aware of the Cathier iOS app workflow (Xcode + fastlane + auto-merge @claude PRs from in-app feedback).

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Designs team Git workflows for branching, PRs, and releases. Use when choosing branching models, stacked PRs, merge queues, worktree isolation for agents, or collaboration rules.

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Planning specialist that breaks a VNX feature or track into small, independently-shippable PRs with dependencies and per-PR task-class routing. USE THIS when the user wants to break a feature down into PRs, sequence the work, or turn a plan into a PR queue. Delegated to by @horizon (formerly @pm — @pm still resolves via alias). Works from Horizon's tracks DB (`vnx horizon`, alias `vnx objective`); the repo FEATURE_PLAN.md is a generated generic example, not the source.

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Use when the user says "atomic PRs" or requests one issue or PR per logical change. Don't use for single-change pushes or uncommitted change-sets.

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Guide for simplifying and refining code after coding sessions. Use when cleaning up complex code, reviewing PRs for readability, or applying consistent refactoring patterns. Triggers on simplify code, refactor, clean up, code review, コード整理, リファクタ, 複雑さ削減, コードレビュー.

Rebuild, re-pin, and republish Pulp's downstream demo/example repos against a new or the latest SDK. Routes natural-language requests — "update the demos to the latest SDK", "rebuild the examples against the new SDK", "check the demos still build on the new SDK", "bump every consumer's SDK pin", "open the SDK-update PRs", "republish the demo packages" — to the `pulp minos` Managed SDK Consumer Sweep: `sweep` (build + measure min-OS floors), `update` (bump each repo's SDK pin, open PRs), and `publish-runbook` (per-repo rebuild/package/publish steps).

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Review Dependabot PRs efficiently: triage, risk assessment, batching, and auto-merge policies. Use when dependency update PRs pile up or you want a sane update workflow.

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GitHub patterns using gh CLI for pull requests, stacked PRs, code review, branching strategies, and repository automation. Use when working with GitHub PRs, merging strategies, or repository management tasks.

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Review and merge student exercise PRs during TP sessions. Arguments: <repo-url> [--class <class-id>] [--timeslot <HH:MM-HH:MM>] [--dry-run]

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GitHub operations via `gh` CLI: issues, PRs, CI runs, code review, API queries. Use when: (1) checking PR status or CI, (2) creating/commenting on issues, (3) listing/filtering PRs or issues, (4) viewing run logs. NOT for: complex web UI interactions requiring manual browser flows (use browser tooling when available), bulk operations across many repos (script with gh api), or when gh auth is not configured.

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Knowledge base from the FAA Systems Engineering Manual (SEM) v1.0.1. Use for civil-agency systems engineering as the FAA practices it inside the Acquisition Management System (AMS) and the National Airspace System (NAS): the five-phase AMS lifecycle and its decision points; operational concept development and implementation-free functional analysis (ConOps, FFBD/N², CMLs); requirements analysis and architectural design synthesis (PRS→MRS, the PRD ratchet pPRD→iPRD→fPRD, RAM, ISEF/DoDAF views, CPRs); the seven technical management disciplines (Integrated Technical Management/SEMP, Interface Management/IRD-ICD, Risk-Issue-Opportunity, Configuration Management, SE Information Management, Decision Analysis, Verification & Validation); and the specialty disciplines (RMA via Service Threads/STLSC, Life Cycle Engineering, E3/Spectrum, Human Factors, Information Security via the NIST RMF, System Safety via the SMS, and Hazardous Materials/Environmental/EOSH). Scope limits: this is FAA-specific guidance, not policy — it is a tailorable menu that points outward to companion handbooks (FAA-HDBK-006A for RMA, the SMS Manual, the NIST 800-series) rather than restating generic SE theory; it is thin on detailed cost estimating, contracting/FAR law, software-development methodology, named anti-pattern catalogues, and any non-FAA or non-civil-aviation lifecycle. Source has no page numbers in the extracted text (~360 pp.).

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AI PR intake and multi-agent governance for deployless repositories. Use when a repo has high-volume bot or agent PRs, parallel agent work, noisy low-context PRs, merge-queue pressure, CI exhaustion, duplicate fixes, ownership confusion, or review bottlenecks that threaten a single-mainline delivery model.

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Operational guide for the three recurring NV oOS maintenance tracks: (1) Docs & Release Catch-Up — plan-first per-version docs, changelog, and version-bump passes; (2) Model Catalog & Config Updates — the monthly model-config refresh across the catalog and its derived files; (3) PR Deferred-Item Sweep — review merged/closed PRs for deferred work and file GitHub issues for what is still incomplete. Use when asked to 'catch up docs', 'update the model configs', or 'review the week's PRs for deferred work'.

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Create a construction plan for a multi-step engineering task that requires multiple PRs or a phased approach. Produces a self-contained plan file with dependency graph, review gates, and step-by-step execution instructions for coding agents. TRIGGER when: user requests a plan, blueprint, or roadmap for a complex task, or describes work that clearly needs multiple PRs. DO NOT TRIGGER when: task is completable in a single PR or fewer than 3 tool calls, user asks to modify/update an existing plan, user says "just do it", or user asks for code review/audit.

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Unified pull request workflow: prepare a safe branch, run read-only review, fix Required findings, create/update a GitHub draft PR, and verify CI plus automated review comments. Subcommands: `create` (simplify + PR, skip code review), `review` (read-only findings only), `fix` (Required fixes + commit, no push), `simplify` (simplification only), `verify` (existing PR checks/reviews only). Use when creating or reviewing PRs, self-reviewing changes, simplifying PR changes, or requesting "PR作成", "レビュー", "簡素化". Do NOT use for responding to review comments or a lightweight review of the current working diff without the PR workflow (use the built-in /code-review instead).

GitHub repository management — triage PRs/issues, check Actions status, manage branch protection, tag releases, housekeeping (stale branches, stashes), CODEOWNERS, badges, and repo hardening. Use when the user asks about GitHub, PRs, CI/CD status, repo health, branch protection, releases, or any GitHub operations.

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Fetch unread GitHub notifications for open PRs where review is requested from a specified team or opened by a team member. Use when asked to "find PRs I need to review", "show my review requests", "what needs my review", "fetch GitHub review requests", or "check team review queue".

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Diagnoses CI and pull-request pipeline health for a GitHub repo using the engineering analytics MCP tools — pull-requests (PR list with CI status), workflow-health (per-workflow CI trends), and pr-lifecycle (a single PR's timeline). Use when asked whether CI is getting faster or slower, which GitHub Actions workflow is the slow or flaky long-pole, how long PRs take from open to merge, how an author's merge time compares to the cohort, which open PRs have failing or pending CI, or where a specific pull request is stuck. Triggers on "engineering analytics", "is CI getting slower", "slow workflow", "flaky CI", "time to merge", "cycle time", "PR throughput", "failing checks", "where is PR <n> stuck", "CI long pole", "what's holding up this PR".

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taskboard の MCP tool（health / board_* / task_* / work_* / doc_* / ask_* / review_request / feedback_list / comment_reply / schedule_* / session_* / orchestrator_* / settings_* / inbox_* / prs_* / usage_get）でタスク・作業項目・文書と、案件・定期起動・セッション・受信箱を扱う。自分のセッションに紐づくタスクの列を進める・起票する時、計画の承認後に作業項目を登録し着手・完了・待ちを更新する時、計画書・設計提案を人に読ませて採否やレビューを求める時、ボードの一覧・状態を確認する時、オーケストレーターとして全体の health を見回る時、案件・定期起動・セッションを作る・変える・止める・消す時、依頼に taskboard・タスクボード・kanban・作業項目の語がある時に使用。境界: taskboard の外で始まったセッションをタスクに移すのは taskboard-adopt、pane・tab・agent の操作は herdr、作業ログ・調査記録はメモリディレクトリ、ボードの画面操作はユーザーの領域、新しい定期起動の中身（仕組みの選択・手順書・プロンプト・状態ファイル）の設計は scheduling-jobs。

抽象的な要件・事業側の要求を深掘りし、既存実装との整合を確認して実装マスタとシステム要件書を作成する。「こういう機能を作りたい」「この要求を満たす機能を設計して」等の抽象要件の提示時、既存機能の拡張や Phase 分割の要件定義開始時、/design-feature 実行時に使用。境界: 要件確定後の実装計画書・PR 分割と実装進行は plan-feature-prs。