「fal」の検索結果

Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT projection, masking no-coverage sites so a consensus does not manufacture false reference calls, or setting iVar min-depth/min-frequency policy for surveillance genomes.

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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-mapping co-regulated TWAS hits, or triangulating TWAS with cis-eQTL Mendelian randomization and colocalization to nominate a causal gene.

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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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If CGM is not available, continue monitoring blood glucose with point-of-care testing as an alternative option. Trigger phrases include: "CGM is not available, what should we use for glucose monitoring?

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In central hypothyroidism patients receiving levothyroxine who initiate enzyme‑inducing antiepileptic drugs, the guideline recommends checking free T4 at least 6 weeks after AED start and increasing the levothyroxine dose if free T4 falls below the target range. Triggers include: central hypothyroidism patient on levothyroxine starting antiepileptic drug such as phenytoin, carbamazepine, or oxcarbazepine.

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Decide when to order coronary artery calcium (CAC) scoring in a primary-prevention patient and interpret the result per the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers the Class 1 indication (men ≥40 / women ≥45, borderline / intermediate PREVENT-ASCVD risk, uncertainty about LLT), CAC score interpretation (0, 1–99, 100–299, ≥300, ≥1000), how CAC modifies LDL and non-HDL goals, when to repeat CAC, and pitfalls (incidental CAC on non-cardiac CT, radiation, cost). Use when a clinician asks should I order a CAC score, CAC indications, what does CAC 150 mean, treatment goals with CAC score, repeat CAC frequency, CAC in a smoker, CAC vs CCTA, is CAC useful in intermediate risk. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.

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Look up NHS England genomic tests for rare and inherited diseases. Use this skill whenever a clinician asks what genetic test to order for a condition, which genes are covered for a specific diagnosis, what commissioning category a genomic test falls under (Core, Specialised, or Highly Specialised), or which tests belong to a specialty group (Neurology, Cardiology, Endocrinology, etc.). Also trigger for questions like what panel is used for a condition, whether there is an NHS test for something, what the R number is for a condition, or whether anything has changed in the genomic test directory. Source: NHS England National Genomic Test Directory for Rare and Inherited Disease v9.0 (April 2026).

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Reconcile baseline-versioned files that the `create-baseline upgrade` CLI staged for LLM-assisted semantic merge. Use when the CLI prints "Open Claude Code and run /upgrade-project to reconcile". Reads the stage manifest at `.claude/state/upgrade/<ts>/manifest.json`, reasons through each pending file's three-way delta in main context, writes a reconciled LOCAL, then deletes the stage when every file lands. Supports `--dry-run` (preview the reconciled diff without writing) and a structured "needs-user-input" fallback when the conflict cannot be disambiguated automatically.

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Use when starting feature work that needs isolation from current workspace or before executing implementation plans - ensures an isolated workspace exists via native tools or git worktree fallback

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Run local AI services on Windows — port binding, firewall, WSL2 networking, and common pitfalls.

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Pitfalls, examples, and edge cases for Hermes Kanban workers. The lifecycle itself is auto-injected into every worker's system prompt as KANBAN_GUIDANCE (from agent/prompt_builder.py); this skill is what you load when you want deeper detail on specific scenarios.

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Every product will be AI-powered. The question is whether you'll build it right or ship a demo that falls apart in production.

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Find and fix WCAG 2.2 accessibility issues. Two modes — report (sweep a codebase or page, produce a prioritized written report, no edits) and fix (audit→edit→verify loop on a target). Prefers direct-CDP live-DOM auditing; falls back to a browser-MCP composition or HTML-string audits.

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Run a Codex prompt repeatedly on a fixed interval. Use for "/loop", "run this every N minutes/hours", "poll X every 5 minutes", "repeat this Codex prompt", or any recurring interval-based Codex job. This is the interval-repeat companion to the separate `schedule` skill (cron / specific-time). For a durable, always-on alternative that survives reboots and terminal exits, prefer Codex app Automations; this local CLI is a terminal fallback that only fires while its daemon process is running.

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Run a Codex prompt on a cron schedule or at a specific future time. Codex app Automations is the official, always-on surface for durable recurring schedules — recommend it FIRST; this local skill is a terminal fallback that only fires while its daemon runs. Triggers include "/schedule", "cron", "every Monday 9am", "run this at 3pm", "schedule a codex prompt", "recurring codex task", and one-time future runs ("run once at 3pm", "remind me to check X tomorrow"). For fixed-interval repeats ("every N minutes"), use the separate `loop` skill instead.

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Write what the work found into the project's knowledge record, so the next session inherits it instead of re-deriving it. Use the moment something worth keeping exists: a fact taken from a source, a rule worked out, a decision or conclusion, a measurement, a correction to a recorded value, or a question left open - and check for unrecorded findings before implementation, handoff (including a PR), or finishing work. Record within the user's write authorization. The first write creates GROUNDING.yaml. Covers one-report update, add, set, review, same and distinct, judgments with a falsifier, and background capture.

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[Workflow] Use when activating the Greenfield Project Init workflow for full waterfall project inception from idea through implementation with integration testing.

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[Planning] Use when you need to start a new project from scratch with full waterfall inception — idea, research, domain modeling, tech stack, and implementation plan.

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[Frontend] Use when you need to extract design context from Figma URLs via MCP, REST API, or screenshot fallback.

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Use when the user asks how to build with OpenAI products or APIs, asks about Codex itself or choosing Codex surfaces, needs up-to-date official documentation with citations, help choosing the latest model for a use case, or model upgrade and prompt-upgrade guidance; use OpenAI docs MCP tools for non-Codex docs questions, use the Codex manual helper first for broad Codex self-knowledge, and restrict fallback browsing to official OpenAI domains.

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Full website GEO+SEO audit with parallel agents first and skills fallback. Orchestrates a comprehensive Generative Engine Optimization audit across AI citability, platform analysis, technical infrastructure, content quality, and schema markup. Produces a composite GEO Score (0-100) with prioritized action plan.

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When editing a module-shaped path (`Modules/*`, `packages/*`, `apps/*`) while `modules.enabled` is false — asks once to enable it; also the project/stack + task-runner detection reference.

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