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Drafts code-compliant California responses to Requests for Production (CCP § 2031.010 et seq.) for Superior Court. Use when the user mentions California RFP responses, CCP 2031, discovery objections, compliance statements, inability to comply, privilege objections, Bates numbering, verification requirements, or responding to document requests in California state court. California Superior Court only — not for federal court without substantial modification.

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Use when a problem requires structured step-by-step reasoning before acting. Prevents jumping to conclusions or guessing root causes without evidence. Triggers on complex debugging, multi-step analysis, hypothesis verification, or when mk:fix invokes diagnosis phase. NOT for being stuck on approach (too many implementations, forced assumptions, innovation block) — use mk:problem-solving instead.

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Test-to-requirement coverage mapping. Reads plan acceptance criteria and test files, produces a coverage gap report showing which requirements have no tests. Use during Phase 2 (Test) or Phase 4 (Review) to verify test completeness. Named after the Nyquist sampling theorem — sufficient test coverage prevents aliased (missed) requirements. NOT for running tests (see mk:testing); NOT for structural code review (see mk:review).

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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.

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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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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.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Orientação de liderança técnica para equipes de engenharia, decisões de arquitetura e estratégia de tecnologia. Inclui analisador de débito técnico, calculadora de escalabilidade de equipes, frameworks de métricas de engenharia, ferramentas de avaliação de tecnologia e templates de ADR. Use ao avaliar débito técnico, escalar equipes de engenharia, avaliar tecnologias, tomar decisões de arquitetura, estabelecer métricas de engenharia ou quando o usuário menciona CTO, débito técnico, débito técnico, escalabilidade de equipes, decisões de arquitetura, avaliação de tecnologia, métricas de engenharia, métricas DORA ou estratégia de tecnologia.

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要件定義と実装の間を埋める技術仕様書を体系的に作成するスキル。 画面設計、API設計、DB設計、シーケンス図、状態遷移図をMermaid形式で生成し、 IEEE 830/ISO 29148準拠の仕様書を出力する。Use when creating functional specifications, API design documents, database design documents, screen design specifications, or sequence/state diagrams from requirements. Triggers: "technical specification", "functional spec", "API design", "database design", "screen design", "画面設計書", "API設計書", "DB設計書", "技術仕様書", "シーケンス図", "状態遷移図"

Clarify ambiguous or conflicting requests by researching first, then asking only judgment calls. Use when prompts say "grill me", ask hard questions, request relentless interrogation, pressure-test assumptions, clarify scope/requirements, define success criteria, or request system-design/optimization decisions before implementation; stop before implementation.

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Create a pull request from the current branch. Triggers on create PR/open PR/make PR/submit PR/push PR/raise PR/open a pull request/create a pull request/ready to merge/branch is ready when the user wants to turn their current branch into a GitHub pull request with a well-structured description

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Análisis de requisitos de documentos: Analiza los documentos de concepto y requisitos en la carpeta docs/, verifica los requisitos con el código actual y crea un informe de diferencias consolidado.

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Document requirements analysis: Analyzes concept and requirements documents in the docs/ folder, checks requirements against current code, and creates a consolidated difference report.

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Prepares a DRAFT internal audit pack from the audit plan: scope as stated, criteria with clauses quoted from the documents provided, document requests per auditee with due dates, open interview questions per process and role, previous findings to follow up and a readiness checklist. Never pre-judges conformity, writes findings or selects the sample; the lead auditor decides. Use when the user asks to "prepare the internal audit", "build the audit pack from this plan", "draft the document requests and interview questions" or "get us ready for the supplier audit". Do not use for evidence requests built from a control list, use control-evidence-request-pack instead; to chase actions from earlier audits, use corrective-action-tracker. Drafts for human review; never approves, authorises or signs off.

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Configures the JetFormBuilder action events system — the named events (DEFAULT.PROCESS, DEFAULT.REQUIRED, GATEWAY.SUCCESS, GATEWAY.FAILED, BAD.REQUEST, ON.DYNAMIC_STATE, never) that decide WHEN a Form Action runs. Covers declaring supported / unsupported / required events on a custom action, the validation precedence inside Base_Event::is_valid_action(), the multi-event subscription model the action editor exposes, and how to register a brand-new event type via the 'jet-form-builder/event-types' filter using Base_Event, Base_Action_Event, or Base_Gateway_Event. Use when an action needs to run only on payment callbacks, only on validation failure, only on a specific conditional state, after another action's hidden flow, or when the plugin needs to define its own event class (e.g. for inbound webhooks). Triggers on mentions of "JFB events", "action events", "GATEWAY.SUCCESS", "DEFAULT.PROCESS", "supported_events", "unsupported_events", "get_required_events", "Base_Event", "Base_Gatewa...

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Ensure requirement docs define scope, terminology, acceptance criteria, edge cases, and non-functional requirements.

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Use this skill when writing a pull request description, change summary, or release notes in Japanese for this project. Trigger words: PR 説明, プルリク, 変更サマリ, リリースノート, PR 文章, レビュー依頼, 日本語で説明, pull request.