「changes」の検索結果

DRY (Don't Repeat Yourself) review rules for code reviews: find the same knowledge — a rule, a constant, a parser, a validation, a protocol detail — implemented in several places that must change together, and tell it apart from code that merely looks alike. Use when reviewing a diff, a pull request or recent changes for duplication, on "DRY review", "is this duplicated", "copy-paste check", or when a review checklist asks for DRY. Pair it with the solid skill for design and with owasp-asvs for security.

日本語の概要は準備中です。原文の説明を表示しています。

Add or update a GEODE model or provider from current primary documentation and repository call-site evidence. Use for model IDs, context limits, pricing, reasoning controls, provider routes, capability gates, or fallback changes.

日本語の概要は準備中です。原文の説明を表示しています。

VitePress documentation workflow for Software Metrics Machine docs under docs/vitepress. Use when creating, updating, reviewing, or restyling SMM documentation pages, especially feature docs that must keep CLI terminal examples and dashboard views/screenshots in sync. Covers Markdown style, VitePress tabs, command examples, dashboard screenshots, sidebar links, and docs validation. USE FOR: docs/vitepress, VitePress docs, documentation style, CLI docs, dashboard docs, screenshots, feature pages. DO NOT USE FOR: application code changes unless needed to verify documented behavior.

日本語の概要は準備中です。原文の説明を表示しています。

Structures git branches and worktrees: keeps unrelated changes on separate branches, isolates each in its own worktree created so the repository's setup runs, records dependencies with git-machete, and recombines them into a temporary mixdown branch for local testing. Use before creating any branch or worktree in a codebase that works on more than one branch, including branching off the default branch to start a change; when starting work in a fork, clone, or third-party checkout; when choosing what a new branch should be based on; when a branch is growing a second unrelated concern; when deciding whether to stack branches or keep them independent; when preparing a change for a pull request or patch submission; when handed an existing worktree or branch to implement and commit in a fork; or when a local build needs several in-progress branches combined. Not needed where the repository clearly commits everything to the trunk, or holds notes or personal data rather than code.

日本語の概要は準備中です。原文の説明を表示しています。

Generates a pull request description for the current branch and writes it as Markdown to .git/magit/posts/new-pullreq for magit-forge. Use when the user asks for a PR description, PR summary, or write-up of what a branch changes, or is preparing to open a pull request.

日本語の概要は準備中です。原文の説明を表示しています。

Adds or changes allowed commands in AI agent permission configs for OpenCode and Claude Code. Use when a command needs adding to an agent's allow list, when permission settings for existing commands need changing, when setting up a new AI tool that requires command permissions, or when the user asks to stop being prompted for a particular command.

日本語の概要は準備中です。原文の説明を表示しています。

Evaluate repeated code and consolidate duplication when a shared abstraction improves correctness or maintenance. Use after introducing similar logic or when repeated changes reveal a missing source of truth.

日本語の概要は準備中です。原文の説明を表示しています。

Stage whole files, selected hunks, or selected lines in Git without interactive prompts. Use when preparing an exact commit boundary while preserving unrelated working-tree changes.

日本語の概要は準備中です。原文の説明を表示しています。

Triages an already-dirty Git working tree: breaks down every uncommitted change hunk by hunk, separates deliberate edits from tool-written churn, possibly accidental reversions, misplaced scope, and sensitive content, asks the user about the ambiguous cases, and proposes an ordered set of commits plus a list of hunks to hold back. Use when the user invokes `/pc` or `$pc`, asks what they should commit, wants their uncommitted changes broken down, or wants commits proposed for a dirty working tree or pile of accumulated local modifications. To plan commit boundaries for a change before or while implementing it, use `incremental-commits` instead.

日本語の概要は準備中です。原文の説明を表示しています。

Review staged changes and create atomic Git commits whose messages match repository conventions. Use when the user asks to commit, write a commit message, or finalize already staged work.

日本語の概要は準備中です。原文の説明を表示しています。

Handle MindIE-SD documentation, governance, contributor workflow, commit or PR conventions, history cleanup, template changes, and version-policy updates with minimal context, fixed review steps, and deterministic output. Use this skill whenever the task touches docs/ 或文档站点内容与配置（Sphinx / Read the Docs / conf.py / index.md / 目录导航 / 首页）、中英文双语配套、治理文档、贡献流程说明、PR/MR 模板或标题正文规范、提交历史整理、版本策略与发布规则。即使用户只说「改个文档」「双语要同步」「commit message 怎么写」「PR 模板加一项」「把提交压一下」「rebase 冲突怎么理」而未提治理规范，也应触发。不负责通用工程实现与仓库默认工作流定义（后者以 AGENTS.md 为准）；Python 格式见 code-standards，Markdown 格式见 markdown-lint。

日本語の概要は準備中です。原文の説明を表示しています。

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

日本語の概要は準備中です。原文の説明を表示しています。

Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).

日本語の概要は準備中です。原文の説明を表示しています。

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

日本語の概要は準備中です。原文の説明を表示しています。

Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

日本語の概要は準備中です。原文の説明を表示しています。

Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

日本語の概要は準備中です。原文の説明を表示しています。

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

日本語の概要は準備中です。原文の説明を表示しています。

Session-scoped edit restriction: blocks Edit/Write outside an allowed path, to scope changes to one module or prevent unrelated fixes. NOT for blocking destructive shell commands (mk:careful).

日本語の概要は準備中です。原文の説明を表示しています。

Plan and implement infrastructure, container, CI/CD, deployment-safety, observability, and rollback changes. Does not read dotenv files or approve/release deployments.

日本語の概要は準備中です。原文の説明を表示しています。

JIRA-side cache + project-context discovery via jira-as, diagnostic-only, no Atlassian state changes. NOT issue CRUD or project admin (mk:jira-admin).

日本語の概要は準備中です。原文の説明を表示しています。

Design and implement backend changes end to end: endpoints, handlers, services, integrations, webhooks, jobs, authenticated access. Routes contracts to api-design-principles, schema to database.

日本語の概要は準備中です。原文の説明を表示しています。

JIRA-side cache + project-context discovery via the jira-as wrapper. Triggers: 'jira cache status', 'clear jira cache', 'discover project context for PROJ'. Diagnostic-only — no Atlassian state changes. NOT for issue CRUD; NOT for project admin (mk:jira-admin).

日本語の概要は準備中です。原文の説明を表示しています。

Plan and implement infrastructure, containers, CI/CD, deployment safety, observability, and rollback changes. Use for Docker, IaC, cloud runtime, Kubernetes, pipeline, deployment, or operational reliability work. Does not read dotenv files or approve/release deployments.

日本語の概要は準備中です。原文の説明を表示しています。

Session-scoped directory edit restriction. Blocks Edit and Write outside the allowed path for the current session only. Use when debugging to prevent accidentally "fixing" unrelated code, or when you want to scope changes to one module. Use when asked to "freeze", "restrict edits", "only edit this folder", or "lock down edits". NOT for blocking destructive shell commands (see mk:careful).

日本語の概要は準備中です。原文の説明を表示しています。