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概要と使いどころ
Persists and restores mid-session workflow progress across context resets. Use when resuming workflows, saving state, or handling context compaction. Triggers on: handoff, save state, resume workflow.
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Coordinate staged or parallel jobs across coding-agent runtimes and subagents: routes by capability/risk, isolates writers in worktrees, arbitrates results. NOT for a single-agent task (mk:cook).
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。
Generate publish-grade SVG+PNG technical diagrams — architecture, data flow, flowchart, sequence, agent-memory, class, ER, state-machine, comparison, timeline, and more — across 8 visual styles. Writes output to tasks/visuals/ or an active plan's visuals/ directory. Requires rsvg-convert (librsvg) for PNG export; degrades gracefully to SVG-only when absent.
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 analyzing harness trace logs to surface recurring failure patterns and suggest harness improvements. Scatter-gather pattern across last N runs with mandatory HITL gate before any change is applied. Triggers on /mk:trace-analyze, "analyze traces", "find patterns in harness runs", or after a model upgrade flagged dead-weight-audit-needed.
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-persistent browser automation via Playwright CLI — form filling, screenshots, data extraction, multi-step flows. Use when the user needs to navigate websites, interact with web pages, fill forms, take screenshots, test web applications, or extract information across multiple requests. NOT for AI-driven long-autonomous flows (see mk:agent-browser); NOT for generating .spec.ts E2E code (see mk:qa-manual).
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。
Persists and restores mid-session workflow progress across context resets. Use when resuming workflows, saving state, or handling context compaction. Triggers on: handoff, save state, resume 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 stuck on approach (not debugging). Strategic unsticking via 7 non-default techniques: simplification cascades, collision-zone thinking, meta-pattern recognition, inversion, scale game, first principles, via negativa. Triggers on complexity spiraling, innovation block, recurring patterns across domains, forced-assumption solutions, scale uncertainty, told-it's-impossible, or bloated systems needing subtraction. For evidence-based root-cause debugging, use mk:sequential-thinking 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。
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。
Create beautiful, accessible user interfaces with shadcn/ui components (built on Radix UI + Tailwind), Tailwind CSS utility-first styling, and canvas-based visual designs. Use when building user interfaces, implementing design systems, creating responsive layouts, adding accessible components (dialogs, dropdowns, forms, tables), customizing themes and colors, implementing dark mode, generating visual designs and posters, or establishing consistent styling patterns across applications.
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。
Coordinates QA workflow across planning, writing, and execution agents. Use when user requests testing, quality assurance, or test documentation.
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。
Persistent, adaptive vector memory for agents on a ruOS desktop — a Rust-native vector database with local semantic embeddings, HNSW retrieval, and graph relationships. Use to remember and recall across sessions with no database server or API key.
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。
Store and semantically search agent memory with ONNX vector embeddings on a ruOS desktop, using the Ruflo CLI. Use to persist patterns/decisions across sessions and recall them by meaning rather than exact key.
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。
Generate multiple angles and shot types of a single product for ecommerce-ready image sets. Produces a coherent set (hero 3/4, front, side, back, detail macro, scale, packaging, in-hand) keeping product identity consistent across shots. Use when the user says "different angles", "product shots", "ecommerce image set", "shot list", "PDP gallery", or needs a multi-view set of one product. Part of the Creative Production set.
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。
Vehicle data through Openapi Automotive - look up cars, motorcycles, insurance and MOT status by license plate across Italy, UK, Germany, France, Spain, Portugal. Use for vehicle technical data and insurance validity checks by plate.
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 the extended Corpo Net range suite across many models on one remote host with parallel isolated range instances, local Langfuse recording, bounded spend, and verified teardown. Use when asked to run, rerun, or scale a Corpo Net campaign; use run-ephemeral-hosts for the host contract and manage-remote-resources for billable resource ownership.
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 the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.
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。
Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody methods cannot resolve, and orthogonal validation (miCLIP/GLORI/m6A-SAC-seq/m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set, reconciling differing peak sets across tools, validating MeRIP peaks against single-base methods, interpreting 5' peaks where m6Am contamination is possible, or recommending a consensus strategy.
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。
Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.
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。
Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.
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。
Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.
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 differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).
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。
Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.
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。
Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.
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。
Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.
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。