「sse」の検索結果

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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。

Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS Catalog Calculator with ancestry-aware reference panels (HapMap3, UKB-LD), Pejaver-style calibration, and PRS-RS reporting standards. Use when computing PRS for cohorts, applying Whiffin-style absolute-risk transformation, assessing cross-ancestry portability (Martin 2017 / Ding 2023 continuous ancestry), or auditing PRS manuscripts against the 22-item PRS-RS reviewer checklist.

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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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.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Use this skill when the user asks about driver fitness-for-duty programs — pre-trip readiness assessment, recognizing impairment from drugs/alcohol/medication/fatigue/mental health, refusing assignments when unfit, supervisor training on fitness assessment, FMCSA recommendations on duty status determination, and how to handle a driver who appears unfit. Reference 49 CFR 392.3 + 392.4.

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Organizing digital life for legacy, emergency access, and death preparedness. Specializes in password management, account documentation, digital asset preservation, and ensuring loved ones can access what they need.

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Apply recognition-primed decision making to agents operating under time pressure, uncertainty, and ambiguous cues. Use for situation assessment, RPD-style action selection, and decision-support design in operational settings. NOT for batch optimization, static planning with full information, or tasks where exhaustive search is cheap and harmless.

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Advanced CV for infrastructure inspection including forest fire detection, wildfire precondition assessment, roof inspection, hail damage analysis, thermal imaging, and 3D Gaussian Splatting reconstruction. Expert in multi-modal detection, insurance risk modeling, and reinsurance data pipelines. Activate on "fire detection", "wildfire risk", "roof inspection", "hail damage", "thermal analysis", "Gaussian Splatting", "3DGS", "insurance inspection", "defensible space", "property assessment", "catastrophe modeling", "NDVI", "fuel load". NOT for general drone flight control, SLAM, path planning, or sensor fusion (use drone-cv-expert), GPU shader development (use metal-shader-expert), or generic object detection without inspection context (use clip-aware-embeddings).

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Plan database migrations before executing them: risk assessment, dependency mapping, multi-service sequencing, rollback budgets, and stakeholder communication plans. Use when deciding HOW to migrate, not when writing the actual DDL. NOT for: writing migration SQL (use database-migration-manager), data ETL pipelines (use data-migration-specialist), query optimization, or ORM configuration.

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Audit or design server-side indexes, directories, reputations, or aggregates that are DERIVED from traffic a platform witnesses (chain heads, run verdicts, heartbeats, publish activity) so that consent gates the derivation, not merely the read: no shadow index over non-consenting principals, post-consent-only evidence windows, retention bounds and delete-propagation into derived rows, activity-oracle threat modeling, and audit-logged ranking discretion. Use when building a capability directory / whois from witnessed activity, a reputation ledger from settled outcomes, vitals aggregation across tenants, or any "the yellow pages can't lie because they index signatures" feature. Keywords: shadow index, derived index, consent gates derivation, activity oracle, phone book not a log, delist propagation, ranking weight audit, k-anonymous aggregate, subpoena surface. NOT for the consent-screen UX and scope-ladder mechanics themselves (use local-first-tenancy-boundary), reputation scoring math and Sybil economics (use agent-identity-continuity-reputation), or discovery-layer architecture L1/L2/L3 (use agent-discovery-directories-guilds).

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Generate, fill, and assemble PDF documents at scale. Handles legal forms, contracts, invoices, certificates. Supports form filling (pdf-lib), template rendering (Puppeteer, LaTeX), digital signatures (DocuSign), and document assembly. Use for legal tech, HR automation, invoice generation. Activate on "PDF generation", "form filling", "document automation", "digital signatures". NOT for simple PDF viewing, basic file conversion, or OCR text extraction.

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。

Apply recognition-primed decision making to agents operating under time pressure, uncertainty, and ambiguous cues. Use for situation assessment, RPD-style action selection, and decision-support design in operational settings. NOT for batch optimization, static planning with full information, or tasks where exhaustive search is cheap and harmless.

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。

Expert in ALL computational collage composition: photo mosaics, grid layouts, scrapbook/journal styles, magazine editorial, vision boards, mood boards, social media collages, memory walls, abstract/generative arrangements, and art-historical techniques (Hockney joiners, Dadaist photomontage, Surrealist assemblage, Rauschenberg combines). Masters edge-based assembly, Poisson blending, optimal transport color harmonization, and aesthetic optimization. Activate on 'collage', 'photo mosaic', 'grid layout', 'scrapbook', 'vision board', 'mood board', 'photo wall', 'magazine layout', 'Hockney', 'joiner', 'photomontage'. NOT for simple image editing (use native-app-designer), generating new images (use Stability AI), single photo enhancement (use photo-composition-critic), or basic image similarity search (use clip-aware-embeddings).

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Expert in cluttering -- the lesser-known fluency disorder characterized by rapid/irregular speech rate, excessive disfluencies, and frequent ADHD comorbidity. Covers differential diagnosis from stuttering, assessment protocols, therapy approaches (rate control, self-monitoring, pragmatic awareness), technology-assisted intervention, and AI tools for people who clutter. Activate on 'cluttering', 'rapid speech disorder', 'speech rate too fast', 'speech disfluency not stuttering', 'disorganized speech', 'ADHD speech problems', 'cluttering vs stuttering', 'speech intelligibility', 'mazed speech', 'telescoping words'. NOT for stuttering-only treatment (overlap is common but they are distinct), hearing disorders, or voice disorders (pitch, resonance).

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Track the full Toulmin epistemic ancestry of every claim produced by a multi-agent swarm. Each agent output is tagged with an argument chain (claim / data / warrant / relationship) derived from SwarmTracer spans and LineageEdge records, so operators can zoom into any sub-claim and see precisely which agents asserted it, what triggered each assertion, and how contradictions propagated or were synthesised away. The SwarmTracer pattern — wrapping the SwarmAgentExecutor to capture spans, record messages, and build a lineage graph — is the concrete runtime substrate. Argumentative lineage lifts that graph into the Toulmin vocabulary so reasoning provenance is both machine-queryable and human-interpretable.

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Design RL simulation sandboxes, trajectory datasets, QLoRA/LoRA adaptation plans, eval harnesses, and rollback unhooks for agents learning specific coding behaviors beyond the base model. Use when building or reviewing tool-use training loops, offline trajectories, reward functions, self-improvement harnesses, or Port Daddy agent behavior curricula. NOT for generic ML tutorials, full model training operations, or production deployment without eval gates and safety unhooks.

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Build a LiveAvatar integration end-to-end — assesses the user's existing stack, recommends the optimal path, and guides implementation. Use when: (1) Building a new LiveAvatar integration, (2) Adding a real-time avatar to an app or site, (3) Connecting LiveAvatar to an existing AI pipeline, (4) User mentions LiveAvatar, real-time avatar, interactive avatar, conversational avatar, or lip-sync avatar, (5) Deciding between Embed, FULL Mode, and LITE Mode, (6) Migrating from HeyGen Interactive Avatar to LiveAvatar.

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This skill should be used when the user wants to "stress-test a design", "challenge an idea", "red team a proposal", "get critical feedback on a design", "validate a design", "adversarial architecture review", "risk assessment", "設計を検証して", "反論をもらいたい", "設計を批判的にレビュー", "デビルズアドボケート", "ストレステスト", "弱点を指摘して", "穴を見つけて", "この設計で良いか", "リスク評価", "設計のアーキテクチャレビュー", or mentions structured adversarial review of a proposal or design. NOTE: Use this for validating PROPOSALS and DESIGNS through adversarial debate, NOT for generic code review, PR review, or normal review requests (use /codex:review or /codex:adversarial-review for those). Also NOT for investigating unknown bugs (use /agent-dialectics:strong-inference for that).

AVFoundation (AVPlayer / AVPlayerLayer / AVPlayerItemVideoOutput / AVAsset) の落とし穴・文書化されていない実装挙動・debugging チェックリストを集約した reference skill。Swift / Objective-C で AVPlayer を使った動画再生 / seek / scrub / frame stepping を実装・debug するときに発火。VLCKit ではなく **AVFoundation 系** の問題に特化。

Performs a comprehensive security review of code changes in a GitHub PR or issue. Checks out the branch, analyzes changed files against a 9-category security checklist, and produces PASS/WARNING/FAIL verdicts. Use when reviewing pull requests for security vulnerabilities, hardcoded secrets, injection flaws, auth bypasses, or insecure configurations. Trigger keywords - security review, code review, appsec, vulnerability assessment, security audit, review PR security.

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Framework-directable information security risk assessment. Identifies threats, evaluates likelihood/impact via a 3x3 matrix, maps findings to any compliance framework, and recommends risk treatment options with prioritization guidance.

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。