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概要と使いどころ
Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or HIBAG imputation. Use when typing for HSCT, solid-organ transplant, neoantigen prediction, PGx screening (B*57:01, B*15:02, etc.), or disease-association studies, with reconciliation across tools and IPD-IMGT/HLA version mismatch handling.
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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), mSINGS, and MANTIS for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.
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Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizumab pan-tumor 2020.
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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
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Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.
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Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields
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Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.
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Interactive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL. Use when searching documentation, managing projects/tasks, or querying indexed knowledge. Provides RAG-powered semantic search, website crawling, document upload, hierarchical project/task management, and document versioning. Always try Archon first for external documentation and knowledge retrieval before using other sources.
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Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.
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Automated cell behavior analysis from microscopy or XR lab recordings. Classifies cell motion phenotypes (migration, proliferation, apoptosis, division, quiescence), computes population-level quantitative metrics (growth rate, migration velocity, directionality index), and emits structured JSON for downstream reporting, plotting, or ELN integration.
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Transition insulin pump to scheduled subcutaneous basal bolus insulin when anticipated hospital length of stay exceeds 1 to 2 days and pump expertise is unavailable. Triggers include: "Patient expected to stay >2 days, should we switch pump to scheduled insulin?
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Screen a hypercalcemic patient for medication- and supplement-induced causes — thiazides, lithium, vitamin D, vitamin A/retinoids, antiestrogens, theophylline, milk-alkali, SGLT2 inhibitors, immune checkpoint inhibitors, denosumab rebound, teriparatide/abaloparatide, foscarnet, ketogenic diet, aluminium. Trigger when a clinician asks "is this hypercalcemia drug-induced", "thiazide hypercalcemia", "lithium hypercalcemia", "denosumab rebound hypercalcemia", "vitamin D toxicity", "milk-alkali syndrome", "SGLT2 hypercalcemia", or any new hypercalcemia where medication review is needed.
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Identifies safe antihypertensive options for hypertensive disorders in pregnancy applicable to PA patients, with gestational age restrictions. Triggers include when managing hypertension in a pregnant or pregnancy-planning PA patient and asking 'What BP meds are safe?' or reviewing medications.
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Recommends initiating intravenous isotonic saline hydration as initial management for hypercalcemia of malignancy (HCM) while awaiting antiresorptive therapy, with fluid rate adjusted according to cardiac function. Triggered when a clinician encounters a patient with HCM (e.g., serum calcium >12 mg/dL, symptoms of hypercalcemia) and seeks immediate measures before specific drugs are available.
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This skill advises regular visual examination of the mouth to monitor for osteonecrosis of the jaw and other dental issues in patients receiving antiresorptive agents. Trigger phrases include initiating bisphosphonate or denosumab therapy and requesting preventive dental care guidance.
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Recommends initiating intravenous bisphosphonate or denosumab for adults with hypercalcemia of malignancy compared with no treatment. Use when a clinician asks about first‑line pharmacologic therapy for HCM or when deciding to start antiresorptive agents.
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This skill suggests using denosumab rather than an intravenous bisphosphonate for adults with hypercalcemia of malignancy. It is triggered when a clinician questions which antiresorptive to choose first or seeks guidance on drug selection for HCM.
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The skill suggests adding a calcimimetic for hypercalcemia of malignancy due to parathyroid carcinoma that persists after intravenous bisphosphonate or denosumab therapy. It is triggered when a clinician notes refractory HCM despite antiresorptive therapy and considers adding a calcimimetic.
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Recommends adding intravenous bisphosphonate or denosumab in adults with hypercalcemia of malignancy due to tumors with high calcitriol levels (e.g., lymphoma) who remain severe or symptomatic despite glucocorticoid therapy. Use when managing lymphoma‑related HCM on steroids and considering escalation of antiresorptive therapy.
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Recommends antihypertensive therapy including mineralocorticoid receptor antagonists (MRAs) for patients with a positive primary aldosteronism (PA) screening test who decline confirmatory testing. Triggers include when a patient has positive screening but refuses additional tests and asks "What should I treat with?" or initiates empiric therapy, with preference for MRAs in typical PA presentations (e.g., spontaneous hypokalemia, resistant hypertension, adrenal tumor on CT).
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Recommends switching specific anti-hypertensive medications to reduce false-positive and false-negative screening results for primary aldosteronism. Triggered when a clinician notes 'The patient is on ACE inhibitors/ARBs' or suspects medication interference with screening results.
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The guideline suggests checking serum magnesium and phosphate levels and repleting if low in patients receiving antiresorptive therapy for hypercalcemia of malignancy. Clinicians should consider this when they note electrolyte abnormalities or inquire about supportive care during bisphosphonate or denosumab treatment.
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Recommends checking and managing vitamin D according to Endocrine Society guidelines to avoid hypocalcemia in patients receiving bisphosphonates or denosumab for hypercalcemia of malignancy. Use when a clinician notes risk factors for hypocalcemia (e.g., low 25‑OH vitamin D, renal insufficiency) and asks about baseline labs before antiresorptive start.
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Suggests genetic counseling for patients with primary adrenal insufficiency (PAI) when a monogenic disorder is suspected. Use when PAI patient presents with early-onset disease, syndromic features, consanguinity, family history, or negative autoimmune antibodies.
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