「threshold」の検索結果

Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017 successor to bPTP; bPTP is Python NOT R), GMYC single/multi-threshold (Pons 2006; Fujisawa 2013), multilocus BPP v4 with prior calibration from data (NOT defaults; Yang 2015), SNAPP + BFD* for SNP delimitation, DELINEATE (Sukumaran 2021) speciation-process modeling to address Sukumaran & Knowles 2017 PNAS critique that MSC delimits structure not species, integrative-taxonomy congruence (Padial 2010; Carstens 2013), Dsuite for introgression testing before sister claims (Malinsky 2021), and Meyer & Paulay 2005 barcoding-gap-absence caveat. Use when delineating species from DNA barcoding data, resolving cryptic complexes, choosing among ASAP/mPTP/BPP/DELINEATE, calibrating BPP priors, distinguishing introgression from ILS, or applying the Sukumaran-Knowles oversplitting correction.

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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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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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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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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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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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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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End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Calculate and interpret the PREVENT-ASCVD risk score (10-year and 30-year) for primary prevention of atherosclerotic cardiovascular disease per the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers inputs required, risk-category thresholds (low <3%, borderline 3–<5%, intermediate 5–<10%, high ≥10%), when to use the 30-year calculation (adults 30–59), and how PREVENT differs from the older Pooled Cohort Equations (lower risk estimates by 40–50%, race-agnostic). Use when a clinician asks what the 10-year ASCVD risk is, how to calculate PREVENT, PCE vs PREVENT, risk category for this patient, does my patient need a statin, 30-year risk calculation, primary prevention risk assessment. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Order and interpret lipoprotein(a) [Lp(a)] measurement at least once in a lifetime, apply the risk-enhancer threshold (≥125 nmol/L or ≥50 mg/dL), and run cascade screening of first-degree relatives for premature ASCVD, familial hypercholesterolaemia, or elevated Lp(a) per the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers the Class 1 lifetime measurement, how elevated Lp(a) affects LLT initiation and intensification, the cascade screening indications, the interaction of Lp(a) with ASCVD risk estimation, and current therapeutic limitations. Use when a clinician asks when to check Lp(a), how often to repeat Lp(a), elevated Lp(a) what next, treatment for high Lp(a), should I screen my patient's family, Lp(a) and statins, cascade screening indications. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Use when you need CRAP score and coverage risk analysis to find high-risk code before refactoring or release. Keywords: CRAP score, risk hotspots, cyclomatic complexity, test coverage gaps, coverage threshold.

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Measure real frontend performance — Core Web Vitals (LCP, CLS, INP), page-load traces, CPU and network throttling, Lighthouse accessibility/SEO scores, and heap growth — using chrome-devtools-mcp against a live browser. Trigger when asked "is the page fast enough", "measure Core Web Vitals", "why is this route slow", "run Lighthouse", "check for a memory leak", before any performance-gated certification (Built for Shopify, Core Web Vitals thresholds, store listing review), and before any launch or traffic-multiplier event. Measurement only — this skill never drives functional journeys.

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Use to iterate a change until tests/quality checks pass — bounded run→revise→re-run gated by a numeric threshold, then a judge confirms. Triggers 'iterate to green', 'keep fixing until tests pass'.

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Iteratively improves a PR (GitHub), MR (GitLab), or shelved changelist (Perforce) until it reaches the repository's configured Greptile merge threshold with zero unresolved actionable comments, or until the five-review maximum is reached. Triggers Greptile review, fixes all actionable comments, pushes/re-shelves, re-triggers review only for new head SHAs unless a 5/5 score is already published, and repeats. Use when the user wants to optimize a PR/MR/CL against Greptile's code review standards without creating runaway review loops.

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[Debugging] Use when analyzing or optimizing performance bottlenecks: database queries, N+1 fan-out, indexing, API latency, memory/GC, concurrency and pool saturation, algorithmic complexity (O(n²)), network/protocol round trips, frontend rendering and Core Web Vitals, caching, and distributed/resilience paths. Calibration constants and domain laws (latency ladder, Little's Law, utilization knee, CWV thresholds, symptom→cause triage) live in references/performance-knowledge.md.

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Maintain stewardship protocol continuity and tool/personality boundaries. Use when a repo agent needs steward-mode threshold checks, self-model update decisions, delegation hygiene, boundary violation review, or handoff-safe continuity context without overclaiming steward personality.

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Produces a deep, honest peer-review of how someone uses Claude Code by statistically analyzing their local session data (~/.claude/usage-data/ and ~/.claude/projects/). Trigger whenever the user asks to review, analyze, audit, or critique their own Claude Code usage, workflow, habits, or skill level — including phrases like "analyze my cc usage", "review my cc sessions", "peer review my cc workflow", "deeper than /insights", or any ask for an honest audit of their AI workflow. Also covers portfolio/hiring-manager framings (e.g. "portfolio for Anthropic/OpenAI/xAI"), but ALWAYS ask the user in Step 0 which version to build (self / hr / both) before running — never silently produce an HR report, because that version goes to outsiders and needs explicit privacy setup. The HTML report is laid out ledger-first for SELF (opening band, output/team/leak/trend ledgers, then peer review, 9-dim scoring, try-this-week, case study, claim-indexed evidence). The HR variant is a recruiter version v1: identity card, earned badges (threshold-based, earned-only), allowlist-filtered output ledger, one case study, and a methodology & scope disclosure — no scores, no peer-review memo, no charts.

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How to MEASURE this repo instead of eyeballing it — interpret the loop-station context-budget trend (history.jsonl, thresholds, the tokenizer-switch gotcha), read a session trace, use the eval ledger (cost-per-success), and pick the right evidence tool (app-shots, smoke-deployed, db-counts, --check modes). Use when asked "is the harness bloating", "how big is CLAUDE.md really", "did this agent run actually succeed", "prove this works", "what evidence do we have", or when tempted to declare a capability (browser, tool) unavailable. For RUNNING the loop-station scripts, defer to the loop-station skill — this skill is interpretation + the wider evidence toolkit.

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