「decision」の検索結果

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.

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This skill provides a way to retrieve information from the AgentScope library for analysis and decision-making.

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Create and train AI learning plugins with AgentDB's 9 reinforcement learning algorithms. Includes Decision Transformer, Q-Learning, SARSA, Actor-Critic, and more. Use when building self-learning agents, implementing RL, or optimizing agent behavior through experience.

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Recommends real-time CGM with confirmatory POC-BG for insulin dosing adjustments in insulin-treated hospitalized adults at high risk of hypoglycemia when resources and training are available. Triggers include: "Should we use CGM for insulin adjustments?" or "Is CGM appropriate for this patient?

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Assists clinicians in determining whether to proceed with social transition for prepubertal youth experiencing gender dysphoria or gender incongruence. Triggers include prepubertal youth with GD/gender incongruence and discussions about initiating social transition.

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Suggests either continuous glucose monitor (CGM) or self-monitoring of blood glucose (SMBG) for pregnant individuals with type 2 diabetes. Triggers include decisions about glucose monitoring methods for pregnant patients with T2DM needing a monitoring strategy.

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This skill recommends that a multidisciplinary team, including an experienced endocrinologist, incorporates patient values and preferences while providing education about treatment options for Cushing’s syndrome. Use when planning treatment for a CS patient requiring coordinated care; triggers include persistent hypercortisolism after transsphenoidal surgery, consideration of bilateral adrenalectomy, radiotherapy, or medical therapy, and need for shared decision‑making.

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This skill provides criteria to distinguish unilateral from bilateral primary aldosteronism using adrenal venous sampling results, including lateralization index, contralateral ratio, and clinical factors. It is triggered after AVS when clinicians analyze results and ask 'Is this unilateral or bilateral PA?' or need to guide treatment decisions.

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Determines unilateral vs bilateral aldosterone excess based on cortisol-corrected aldosterone ratios from adrenal venous sampling, with ratio >4:1 indicating unilateral excess, ratio 3:1 suggestive of bilateral hypersecretion, and interpretation dependent on cosyntropin stimulation protocol used during sampling. Use when analyzing AVS results to guide surgical vs medical treatment decisions; triggers include 'AVS lateralization ratio', 'cosyntropin-stimulated AVS', 'aldosterone-to-cortisol ratio >4:1', and 'ratio 3:1 suggestive of bilateral disease'.

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Suggests using longer-acting glucocorticoids when standard hydrocortisone regimens are impractical due to nonavailability, poor adherence, or need for once-daily dosing. Triggers include glucocorticoid replacement therapy decisions where patients report difficulty with multiple daily doses, lack of access to hydrocortisone, or preference for simplified regimens.

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Decide whether a kidney from a brain-dead deceased donor (DBD) with diabetes mellitus and/or hypertension is suitable for transplantation, using the ISOT 2025 Delphi consensus and Table 4 eligibility checklist. Trigger when a clinician asks "can I use a kidney from a diabetic deceased donor", "is this DBD with HTN/DM acceptable", "ECD donor with diabetes — accept or decline", "DBD eligibility for hypertensive donor", or shares a deceased donor with diabetes or hypertension and needs an accept/borderline/decline decision.

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Guide pre-endoscopy management decisions for patients on GLP-1 receptor agonists (semaglutide, tirzepatide, liraglutide etc.), deciding whether to proceed, delay, or modify the approach based on GI symptoms, fasting status, and indication. Trigger when a clinician asks about GLP-1 RA and endoscopy, semaglutide before colonoscopy, Ozempic before procedure, or whether to hold a GLP-1 agonist before endoscopy.

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Write executable failing tests from a recipe handed to you by the main context. Used by `/tdd` Step 2 and ad-hoc when a phase needs tests-first to drive implementation. Decisions about which scenarios to cover, which categories matter, and which fixtures to use are made by the caller — this skill executes that recipe with code-structure discipline.

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Review the auto-extracted candidates in `.claude/memory/_pending.md` and commit keepers to the canonical memory files (`landmarks.md`, `libraries.md`, `decisions.md`, `landmines.md`, `conventions.md`, `pending-questions.md`, `backlog.md`). Invoke at session start when the SessionStart hook reports pending candidates, or any time `_pending.md` has accumulated entries you want to curate. Reset the pending body after flushing.

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Write the production code that makes a pre-decided set of failing tests pass, within an explicit write_set, following an explicit behavior contract. Used by `/tdd` Step 3 and by `/swarm-dispatch` workers. The caller has already decided architecture, naming, file layout, and abstraction boundaries — this skill executes that recipe with code-structure discipline and a 5-iteration RALPH loop. No scope expansion, no design decisions, no test edits.

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Workflow Phase 2 — Codebase Scouting and Constraint Discovery. Maps the relevant slice of the codebase for a given task. Produces a scout report at `docs/scout/<slug>.md` naming the files, modules, and patterns the proposed work touches or constrains. Report decisions execute in main context with full conversation visibility; gathering MAY be delegated to read-only advisory subagents (seed.md §4.2-A).

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Use for Six Thinking Hats or de Bono's parallel thinking, or when a decision or idea needs facts, gut feel, risks, benefits and new options kept apart: "look at this from all sides", "full perspective check". Skip for plain factual questions or single-angle hot takes.

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Use when the user describes a problem, decision or stuck situation but names no method: "how should I approach this?", "help me think this through", "we can't decide", "where do I start?". Picks the best-fit thinking method and runs it. Skip for plain execution tasks or when a method is named.

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