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概要と使いどころ
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.
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Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.
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Recommends discontinuation of GLP-1RA before conception rather than between start of pregnancy and end of first trimester for individuals with type 2 diabetes who are planning pregnancy. Trigger when clinician considers stopping GLP-1RA therapy in a patient with type 2 diabetes who is planning pregnancy or seeking preconception care.
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Recommends mineralocorticoid receptor antagonists for all primary aldosteronism patients to prevent target organ damage, irrespective of blood pressure control or serum potassium levels. Triggered when a clinician encounters a PA patient with well‑controlled BP and normal K and wonders, 'Do I still need to treat with MRA?' or considers stopping therapy.
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Recommends confirmatory testing with corticotropin stimulation test in patients presenting with clinical symptoms or signs suggesting PAI (e.g., fatigue, hypotension, hyponatremia, hyperpigmentation) when the patient's condition permits safe testing. Use when a clinician identifies suggestive features and circumstances allow outpatient stimulation testing without imminent need for emergency glucocorticoids.
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Recommends equipping every patient with primary adrenal insufficiency (PAI) with a glucocorticoid injection kit for emergency self‑administration and providing training on its use. Trigger when preparing a PAI patient for stress dosing, adrenal crisis prevention, or when prescribing glucocorticoid replacement and needing to ensure emergency preparedness.
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The Endocrine Society recommends a standard-dose corticotropin (ACTH) stimulation test to confirm primary adrenal insufficiency when clinical suspicion arises from symptoms such as hypotension, hyponatremia, hyperkalemia, or unexplained fatigue. Dosing is weight/age based: 250 µg for adults and children ≥2 years, 15 µg/kg for infants, and 125 µg for children <2 years.
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Recommends measurement of plasma ACTH to establish primary adrenal insufficiency (PAI) diagnosis in patients with confirmed cortisol deficiency; a plasma ACTH concentration ≥2-fold the upper limit of the reference range supports PAI. Use when evaluating plasma ACTH in a patient with low morning cortisol or abnormal corticotropin stimulation test.
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Performs corticotropin stimulation test to diagnose adrenal insufficiency when morning cortisol is indeterminate (3-15 µg/dL). Triggers include morning cortisol 3-15 µg/dL requiring further AI testing.
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The primary tool for code-navigation questions in ANY language (frontend or backend) — walk the structural graph from an entry point (page, route, handler, command, `main`) down through imports to the IO boundary (network call, query, file read). Use this skill, in preference to the Explore agent or global grep, whenever the user asks "where does X come from?", "what API/data populates Y?", "what renders or wraps the Z panel?", "which file for feature F?", "how is this wired up?", or any code-navigation question mapping a UI element, route, or feature concept to source files. Also reverse queries ("what uses /api/foo?", "who consumes this service?"). Keyword search routinely picks up unrelated flows sharing a domain word and produces wrong answers; the walk follows the actual graph. The JS/TS `walk.mjs`/`discover.mjs` are an optional accelerator, not required — the walk is language-agnostic.
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Split a dirty working tree into single-concern Conventional Commits. The deterministic inventory.mjs helper groups dirty paths by concern (docs, source + paired test, config, governance); main context refines the grouping and presents a commit plan. Read-only until the user approves the plan — it never stages, never commits, never touches consent paths. Disjoint from the commit skill (Phase 11 executor): the planner proposes a split; the executor lands one consented commit. Use when a working tree has accumulated heterogeneous changes that should not land as one commit.
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Extract data from websites, including JavaScript-rendered SPAs and dynamic content
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Integrate TinyFish web toolkit (search, fetch, browser automation) into Hermes Agent
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Records decisions and documentation. Use when making architectural decisions, changing public APIs, shipping features, or when you need to record context that future engineers and agents will need to understand the codebase.
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Prepares production launches. Use when preparing to deploy to production. Use when you need a pre-launch checklist, when setting up monitoring, when planning a staged rollout, or when you need a rollback strategy.
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Azure AI Vision Image Analysis SDK for captions, tags, objects, OCR, people detection, and smart cropping. Use for computer vision and image understanding tasks.
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Build image analysis applications with Azure AI Vision SDK for Java. Use when implementing image captioning, OCR text extraction, object detection, tagging, or smart cropping.
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Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
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Automate web scraping and data extraction with Apify -- run Actors, manage datasets, create reusable tasks, and retrieve crawl results through the Composio Apify integration.
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Extract product data, prices, reviews, and seller information from any e-commerce platform using Apify's E-commerce Scraping Tool.
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Use when assessing AI/ML systems for prompt injection, jailbreak vulnerabilities, model inversion risk, data poisoning exposure, or agent tool abuse. Covers MITRE ATLAS technique mapping, injection signature detection, and adversarial robustness scoring.
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Fetch any X/Twitter post as clean LLM-friendly JSON. Converts x.com, twitter.com, or adhx.com links into structured data with full article content, author info, and engagement metrics. No scraping or browser required.
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