「sequence」の検索結果

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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Refactor Spring Boot and Java code to improve maintainability, readability, and adherence to enterprise best practices. This skill transforms messy Spring Boot applications into clean, well-structured solutions following SOLID principles and Spring Boot 3.x conventions. It addresses fat controllers, improper transaction boundaries, field injection anti-patterns, and scattered configuration. Leverages Java 21+ features including record patterns, pattern matching for switch, virtual threads, and sequenced collections.

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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

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When the user wants help with revenue operations, lead lifecycle management, or marketing-to-sales handoff processes. Also use when the user mentions 'RevOps,' 'revenue operations,' 'lead scoring,' 'lead routing,' 'MQL,' 'SQL,' 'pipeline stages,' 'deal desk,' 'CRM automation,' 'marketing-to-sales handoff,' 'data hygiene,' 'leads aren't getting to sales,' 'pipeline management,' 'lead qualification,' or 'when should marketing hand off to sales.' Use this for anything involving the systems and processes that connect marketing to revenue. For cold outreach emails, see cold-email. For email drip campaigns, see email-sequence. For pricing decisions, see pricing-strategy.

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When the user wants to write, rewrite, or improve marketing copy for any page — including homepage, landing pages, pricing pages, feature pages, about pages, or product pages. Also use when the user says "write copy for," "improve this copy," "rewrite this page," "marketing copy," "headline help," "CTA copy," "value proposition," "tagline," "subheadline," "hero section copy," "above the fold," "this copy is weak," "make this more compelling," or "help me describe my product." Use this whenever someone is working on website text that needs to persuade or convert. For email copy, see email-sequence. For popup copy, see popup-cro. For editing existing copy, see copy-editing.

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When the user needs marketing ideas, inspiration, or strategies for their SaaS or software product. Also use when the user asks for 'marketing ideas,' 'growth ideas,' 'how to market,' 'marketing strategies,' 'marketing tactics,' 'ways to promote,' 'ideas to grow,' 'what else can I try,' 'I don't know how to market this,' 'brainstorm marketing,' or 'what marketing should I do.' Use this as a starting point whenever someone is stuck or looking for inspiration on how to grow. For specific channel execution, see the relevant skill (paid-ads, social-content, email-sequence, etc.).

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Analyze content sequences within a section and provide neutral descriptions for AEM Edge Delivery Services. Invoked per section during page import to identify breaking points between default content and blocks.

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Create, implement, deploy, and debug Adobe Runtime actions with consistent layout, validation, and error handling. Use this skill whenever the user needs to add actions to an App Builder project, understand action structure (params, response format, web/raw actions), configure actions in the manifest, use App Builder SDKs (State, Files, Events, database), deploy and invoke actions via CLI, debug action issues, or implement patterns such as webhook receivers, custom event providers, journaling consumers, large payload redirects, action sequence pipelines, and Asset Compute workers. Also trigger when users mention serverless functions in Adobe context, action logging, IMS authentication for actions, or cron-style scheduled actions.

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Analyze content sequences and determine authoring approach (default content vs blocks). Validates block selection and section styling for import/migration to AEM Edge Delivery Services.

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Generate Mermaid diagrams from code, architecture, or concepts. Use when you need to visualize code flow, system architecture, data relationships, state machines, sequences, class structures, or any other diagrammable concept.

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Runtime security for agent skills — prevents state corruption, skill overwrite attacks, denial of service, and enforces provenance tracking and no-go repo management. Load as part of the secure-* skill sequence whenever an agent processes external content or writes to the skill store. Also load when the user asks to check for state corruption, prevent skill overwrite, manage no-go repos, check provenance, audit runtime security, detect DoS patterns, or protect the skill store. Covers Issues 6, 9, 10 from the agent security threat model: instruction hierarchy enforcement, state corruption and skill overwrite, and denial of service prevention.

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Content sanitization and hidden-content detection for agent skill security. Scans markdown, HTML, and text for visually hidden but agent-readable attacks: CSS-hidden text (display:none, color:white, font-size:0, opacity:0), HTML comments with instructions, collapsible details sections, zero-width unicode, homoglyphs, misleading links, and inline HTML in markdown. Enforces mandatory sanitization before external content enters agent context. Load as part of the secure-* sequence during any repo scan or skill audit. Also load for sanitize content, check hidden text, scan markdown attacks, strip HTML, detect invisible instructions, check zero-width chars. Core principle: visibility does not equal influence — hidden content is more dangerous than visible content because agents process it but humans cannot see it.

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Security audit orchestrator for agent skills — scans for prompt injection, data exfiltration, credential theft, supply chain risks, and instruction hierarchy violations before any skill is installed, created, improved, or read from a GitHub repo. Load when creating skills from external sources, when improve-skills reads from GitHub repos, when research-skill fetches community SKILL.md files, when a user installs a third-party skill, or when the user asks to audit skill security, scan for injection, check if a skill is safe, scan all skills, or run a security sweep. Orchestrates all secure-* skills in sequence. Content is SAFE only if ALL secure-* skills return SAFE. 36% of community skills contain flaws (Snyk ToxicSkills 2026). This skill is the first line of defense.

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Security checks for repository ingestion — scans repos for poisoned examples, dependency and supply-chain attacks, file/path traversal, format-based attacks, and enforces quarantine-before-commit. Load as part of the secure-* skill sequence whenever an agent reads, ingests, or learns from a GitHub repository. Also load when the user asks to check a repo for poisoned code, scan dependencies, verify supply chain safety, check for path traversal, scan repo files for attacks, or audit a repo before ingestion. Covers Issues 3, 4, 7, 8 from the agent security threat model: poisoned training data, dependency attacks, file/path attacks, and format-based attacks.

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Route user requests to the right skill, decompose complex work into parallel subagents, and manage project phase transitions. Load when the user asks "what should I do next", "which skill should I use", "orchestrate this", "run the full workflow", "split this into parallel tasks", or when a complex request spans multiple skills. Also triggers on "coordinate agents", "parallel execution", "task decomposition", "agent workflow", "what phase am I in", or when the user gives a broad instruction that requires multiple skills in sequence. This is the project's brain — it decides what runs, when, and whether to parallelise.

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Create a detailed, step-by-step implementation plan for a feature or project. Load when the user asks to plan a feature, create a technical roadmap, break down a PRD into tasks, design an implementation strategy, or sequence engineering work. Also triggers on "how should we build this", "implementation plan for", "technical breakdown", "task list for", or any request to turn a high-level requirement into a concrete execution plan. Supports phased rollouts, architecture-first, and MVP-focused planning.

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Build GSAP JavaScript animations for web apps — timelines, scroll-driven motion, SVG draw/morph/path effects, and React integration with useGSAP. Load when the user asks to animate with GSAP, add ScrollTrigger, draw SVG paths with GSAP, morph SVG shapes, sequence page animations, or wire GSAP in React/Next/Vue. Also triggers on "GSAP timeline", "DrawSVG", "MotionPath", "gsap.context", or "scroll animation library". Not for self-contained README/GitHub SVG files.

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Orchestrate one or more thinking frameworks to work through any problem, decision, document, or idea rigorously. Diagnoses which frameworks fit — inversion, pre-mortem, assumption-mapping, socratic, adversarial-hat — then guides the user through them in the right sequence. Load when the user asks for deep thinking, says "help me think through this properly", "apply your best thinking frameworks", "I need to think carefully before deciding", or "what thinking tools should I use here". Also the entry point for any complex problem where the right framework is unclear. Covers product decisions, engineering tradeoffs, personal decisions, strategy, creative challenges — any domain.

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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

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Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX (GenBank-submission-mandatory), FCS-adaptor, and BlobToolKit blob plots; and MAG/bin quality assessment with CheckM2 plus GUNC (chimerism) plus GTDB-Tk taxonomy, judged against MIMAG. Covers why CheckM2 alone is blind to disjoint-marker chimeras, the FCS-GX RAM wall, organelle/NUMT triage, strain heterogeneity, and the HGT-vs-contamination (tardigrade) trap. Use when screening an assembly for foreign contamination before GenBank submission, assessing MAG completeness/contamination/chimerism, deciding which contigs to remove, or distinguishing real HGT from contaminant contigs.

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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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。