2,353 件 ・ 関連度順
概要と使いどころ
Fast parallel codebase scouting — searches many directories at once, returning a file map + architecture fingerprint. Use before planning or cross-dir work. NOT for deep single-file reads.
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Deep multi-source technical research with citations — tech evaluation, ecosystem/standards comparison. NOT for API docs (mk:docs-finder), codebase discovery (mk:scout), or project Q&A (mk:ask-me).
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 for deep Vue 3 best-practices review, recommendations, and the full ordered authoring workflow — built-in components (Teleport, Suspense, KeepAlive, Transition, TransitionGroup), animation techniques, slots, fallthrough attrs, custom directives, async components, render functions, plugins, and the post-functionality performance pass. Complements mk:vue (the everyday Composition API quick-reference). Invoke for "review my Vue", "Vue best practices", "recommend improvements", or non-trivial feature work needing the ordered workflow.
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 writing, reviewing, or refactoring Vue 3 code — components, composables, reactivity, Pinia state, Pinia Colada data-fetching, file-based routing, and forms. Targets Composition API + <script setup> + TypeScript. Auto-activates on .vue files. For deep best-practices review/recommendations or the full ordered workflow (built-in components, animations, performance pass), use mk:vue-best-practices.
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。
Reviews a GitHub PR with a single shallow correctness/security/breaking/AI-slop checklist and emits a verdict; optionally posts it via gh pr review. Use to review an external or teammate PR. NOT for deep pre-landing audit of your own diff (see mk:review); NOT for responding to received review comments (see mk:respond-pr).
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。
Structured second-pass reasoning after code review or plan evaluation. Offers named reasoning methods (pre-mortem, inversion, red team, Socratic, etc.) to re-examine findings through a specific lens. Use after /mk:review verdict or any time deeper analysis is needed on an existing output. NOT for initial review (see mk:review); NOT for creating implementation plans (see mk:plan-creator).
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。
Deep spec analysis on a Confluence page. Reads page (+ children) via the confluence-as wrapper, produces a structured Spec Research Report with requirements, acceptance criteria, gaps, ambiguities, and suggested user stories for human review. Read-only — does NOT create Jira tickets. Triggers: 'analyze spec for PAGE-ID', 'extract requirements from confluence page', 'spec research on URL'. NOT for raw page CRUD (mk:confluence-page); NOT for ticket complexity scoring (mk:planning-engine).
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。
Chief Security Officer mode. Infrastructure-first security audit: secrets archaeology, dependency supply chain, CI/CD pipeline security, LLM/AI security, skill supply chain scanning, plus OWASP Top 10, STRIDE threat modeling, and active verification. Two modes: daily (zero-noise, 8/10 confidence gate) and comprehensive (monthly deep scan, 2/10 bar). Trend tracking across audit runs. Use when: "security audit", "threat model", "pentest review", "OWASP", "CSO review".
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。
10-team parallel deep analysis with cross-verification for any topic, repository, or technology. Use when user invokes /research or asks for comprehensive research.
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。
Research-validated planning — research → plan → verify cycle for high-confidence implementation plans
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。
Multi-angle release quality verification using parallel expert review teams
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。
Disciplined goal-to-execution workflow for any user task. Parses objective, asks only for materially missing requirements via ambiguity-gate, inspects repo via idea, plans via sdd-dev or deep-plan, executes safely under project conventions, verifies completion per R020, and reports changed files with evidence. Use when user invokes /goal <task>.
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。
Research complex questions and synthesize relevant evidence into a clear, cited answer. Useful for competitive and market analysis, company research, prospect discovery, enrichment, historical comparisons, and evaluating conflicting claims. Adapt the depth and format to the question; use when a focused search or single-page read is insufficient.
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。
Run an extremely strict maintainability review for abstraction quality, giant files, and spaghetti-condition growth. Use for a thermo-nuclear code quality review, thermonuclear review, deep code quality audit, or especially harsh maintainability review.
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。
Find deepening opportunities in a codebase, informed by the project's own domain language and prior design decisions. Use when the user wants to improve architecture, find refactoring opportunities, consolidate tightly-coupled modules, or make a codebase more testable and AI-navigable.
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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.
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 alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda scheduling, soft-core potentials, MBAR/BAR analysis, cycle-closure validation, and protocol-appropriate enhanced sampling. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.
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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.
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 pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.
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。
Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.
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 direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.
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。
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.
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。
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.
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。
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.
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。