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概要と使いどころ
Set up Claude Code hooks to block dangerous git commands (push, reset --hard, clean, branch -D, etc.) before they execute. Use when user wants to prevent destructive git operations, add git safety hooks, or block git push/reset in Claude Code.
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Managing third-party dependencies — version pinning, security auditing, license compliance, update workflows, lockfile management, supply chain security. Activate on "npm audit", "dependabot", "renovate", "pin versions", "dependency update", "supply chain", "license compliance", "lockfile", "security advisory", "typosquatting", "SBOM". NOT for internal monorepo package management (use monorepo-management) or publishing your own packages to npm/PyPI.
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Use when applying Cloudflare D1 migrations, fighting Supabase migration history vs SQL execution, choosing direct psql over CLI, designing idempotent migrations, debugging schema drift between local and remote, or recovering after a half-applied migration. Triggers: supabase migration repair instructions appearing, table missing after "applied" status, "Tenant or user not found" when running psql, --remote vs --local D1 confusion, NOT NULL on a populated column, foreign key constraint failures, drift between staging and prod schemas. NOT for Mongo/document migrations, ORM-managed migrations specifically (Prisma/Drizzle have their own conventions), or pure data backfills.
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Implement randomization methods for RCTs. Use when user mentions: random assignment, treatment allocation, stratification, blocking, permutation randomization, cluster randomization, randomization balance, misfit handling, re-randomization.
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Reports how local Git branches are progressing toward canonical upstream inclusion as a compact terminal table plus a browser-rendered HTML report, with branch purpose, stack dependencies, Git Machete topology, ahead/behind counts, change-request status, and next action. Use when asked for upstreaming status, local branch submission progress, which branches have change requests, or what remains before they can land.
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Applies local lessons to every use of the Orca CLI (orca-ide, orca-dev). Use alongside the upstream orca-cli skill whenever the Orca CLI is needed, including before creating a branch worktree or asking the user for feedback on a change before committing while running inside Orca.
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。
Gives a repository one idempotent, repo-local worktree setup script (local env files, dependency install, build steps) that worktrunk's `.config/wt.toml` pre-start hook and Orca's `orca.yaml` scripts.setup both call, so every new git worktree is usable at once. Use when adding or fixing worktree setup hooks, writing `wt.toml` or `orca.yaml` setup, when new worktrees lack dependencies or `.env` files, or when asked to make worktrees "just work" in a repo. For creating a worktree in a repo that already has setup, use `git-branch-management` 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。
Applies local reliability, viewport, tab-safety, stale-ref, widget, and browser-boundary lessons to every agent-browser automation. Use alongside the upstream agent-browser skill whenever navigating, clicking, filling, testing, extracting, taking screenshots, or debugging any website with agent-browser.
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。
Open a URL or local file in the user's regular browser, including live-rendered local Markdown. Use for `/open` or when the user asks to view a target outside the agent browser.
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。
Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.
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。
Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the critique that "n=3" is a publication convention rather than a power calculation. Use when budgeting a sequencing experiment, writing the sample-size justification in a grant, estimating replicates from pilot data, allocating a fixed budget between samples and depth, or planning scRNA-seq cohort size. For clinical-trial sample size see clinical-biostatistics/power-and-sample-size; for the power-given-n direction see experimental-design/power-analysis.
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。
Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.
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 genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.
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。
Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.
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 recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-level analysis, q-values from permutation) and quantify copy-number signatures with the Steele 2022 COSMIC framework and the Drews 2022 CINSignatures framework. Covers driver-gene localization from recurrence peaks, distinguishing focal drivers from arm-level passengers, and the caller-sensitivity caveats of copy-number signatures. Use when finding recurrently amplified or deleted regions in a cohort, localizing driver genes, separating focal from broad events, running GISTIC2, or extracting copy-number mutational signatures.
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。
Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.
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 gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-mapping co-regulated TWAS hits, or triangulating TWAS with cis-eQTL Mendelian randomization and colocalization to nominate a causal gene.
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。
Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.
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。
Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/screenpipe) running locally on port 3030 — the skill has no other data source and will refuse to run if screenpipe is unreachable. All detection runs locally; only redacted cluster summaries reach the LLM.
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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。
Use when a plan directory (plan.md + phase-*.md) needs a visual review. By DEFAULT this drives the STRUCTURED visual-plan artifact (visual-plan/plan.json) via the mewkit visual-plan CLI — generate if absent, validate, open the local studio (view/edit), and export plan.html from the approved artifact. Pass --static for the legacy prompt-only single-file plan.html template render. Triggers on "render this plan", "visualize the plan", "open the plan studio", "make a shareable plan page", "plan.html". This is the canonical owner of plan-as-visual-review. NOT for plan critique or scope review (see mk:plan-ceo-review / mk:validate-plan), NOT for generic code/diagram/diff visuals (see mk:preview), NOT for live media generation (see mk:multimodal).
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。
Serve any markdown file or directory as a calm, book-like reader via a local HTTP server (127.0.0.1 only). Best for long-form documents — RFCs, runbooks, design docs, plan files — where comfortable in-browser reading matters. Supports Mermaid diagrams, dark/light mode, plan navigation sidebar, and keyboard shortcuts. Requires explicit start and stop lifecycle.
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。
Use RoutIR — call a running endpoint with the client, stand up a local server that mixes locally-hosted services with services proxied from a remote master server, and extend RoutIR with new bi-encoders, rerankers, and document collections by writing a small config (and optionally one Python file referenced via `file_imports`). No checkout of the routir source is required.
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。