'fix' 검색 결과

Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.

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Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant surveillance for SARS-CoV-2 / influenza / Mpox / RSV / H5N1 / measles.

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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Run build, deploy, inspect, and fix loops for .NET MAUI apps that already have MAUI DevFlow integrated. USE FOR: launching MAUI apps, selecting devices or emulators, waiting for or recovering agent connections, broker/port/adb connectivity issues, visual tree inspection, screenshots, UI interaction, Blazor WebView CDP debugging, reading DevFlow logs, and iterative app debugging. DO NOT USE FOR: first-time DevFlow package setup (use maui-devflow-onboard), or generic desktop automation unrelated to MAUI. INVOKES: maui devflow CLI, dotnet CLI, Android adb/android tools, and Apple simctl tools.

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Use this skill when the user asks specifically about preparing for the New Entrant Safety Audit (NESA) under 49 CFR 385 Subpart D — different from a Compliance Review. Covers what auditors look at, the 18-month window, automatic failure conditions, the 60-day fix window, what to NOT do, and how to convert from "new entrant" to permanent authority. Cite 49 CFR 385.301-321.

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Use when a carrier asks how to calculate cost-per-mile (CPM) at the fleet, truck, lane, or driver level — separating fixed vs variable costs, allocating overhead, accounting for empty miles, and using CPM to negotiate rates, build pricing tiers, or evaluate lane profitability.

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Audit designs, color palettes, and UI components for WCAG 2.1 accessibility compliance, providing specific fixes for contrast, touch targets, focus indicators, and screen reader support. NOT for color harmony aesthetics or design system creation.

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Classify every destructive/gated action an agent body can attempt (git, filesystem, network, shell, github) into block/approve/allow tiers, and audit whether the pre-tool and post-tool governance backing that classification is real: blocked actions proven zero-side-effect by a negative fixture, every denial backed by a receipt and a transcript event, every block-tier denial paired with a safe alternative, and no unmanaged or same-UID body ever marked "contained." Use when building or reviewing Agent Harbor's C5 governance gate (destructive git blocker, approval request/result, denial receipts), gating a new tool surface before it can run destructive commands, or auditing whether an existing "destructive-action blocked" claim actually has evidence behind it. NOT for proving an existing sandbox boundary actually contains an adversary once an action is isolated (use sandboxed-adversarial-test-harness), deciding where in a DAG to place a human review node or designing the approval UX itself (use human-gate-designer), or designing the general work-receipt schema across an entire agent task (use agent-work-receipt-designer).

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Decides HOW to mutate a DAG when a node fails, quality is below threshold, or new information changes the plan. Selects from mutation strategies (add node, replace agent, fork paths, loop back, downgrade model) based on failure type, cost budget, and execution history. Activate on "DAG failed how to fix", "mutation strategy", "replan on failure", "adaptive DAG", "recovery strategy", "what to do when node fails". NOT for detecting failures (use dag-quality), executing mutations (use dag-planner), or runtime execution (use dag-runtime).

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Use when designing or fixing a Content Security Policy on a real site, choosing between nonce-based and hash-based CSP, adding strict-dynamic, debugging "Refused to execute inline script" errors, deploying CSP in report-only mode first, configuring report-to / report-uri, or auditing an existing policy for unsafe-inline / unsafe-eval / wildcards. Triggers: "CSP blocks legitimate inline script", strict-dynamic, nonce-{RANDOM}, sha256-{HASH}, object-src none, base-uri none, frame-ancestors, Trusted Types, X-Content-Security-Policy obsolete, report-only vs enforced. NOT for general HTTP security headers (HSTS, COOP/COEP), Trusted Types deep dive, CORS configuration, or building a WAF.

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Interprets GitHub Actions run status and logs, diagnoses CI failure patterns, and suggests targeted fixes. Handles dependency install failures, test timeouts, build OOM, flaky tests, and workflow misconfigurations. Activate on: 'CI failing', 'build broken', 'workflow error', 'GitHub Actions debug', 'flaky CI', 'pipeline timeout', 'CI red'. NOT for: writing new workflows from scratch (use github-actions-pipeline-builder), CI caching strategy (use ci-cache-optimizer), deployment orchestration (use devops-automator).

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Detects and fixes color contrast violations using WCAG 2.1 guidelines and perceptual analysis. Expert in contrast ratio calculation, color blindness simulation, and providing accessible alternatives. Activate on "check contrast", "color accessibility", "WCAG audit", "readability check", "contrast ratio", "hard to read", "can't see text". NOT for general color theory (use color-theory-palette-harmony-expert), brand color selection (use web-design-expert), or non-visual accessibility (use ux-friction-analyzer).

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Russell Beale's "Rise up, Revolt!" analysis of why users blame themselves for bad design, and how consciousness-raising (not designer education) is the lever that fixes usability at a market level

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Design an agent's handling of obligations, prohibitions, permissions, and conflicts among norms and goals. Use when an autonomous agent must decide which norms apply and what to do when they conflict. NOT for simple fixed policy checks, ordinary BDI commitment design, or organizational metaphor.

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Author a pull request an AI coding agent can actually get merged: a scoped, coherent diff; a Summary and Test Plan backed by real evidence; correct triage of required-and-blocking CI gates versus external/advisory checks (e.g. a Cloudflare Pages preview build); draft-while-WIP discipline; named fixup commits for real review findings; and a clean landing through a merge queue without force-pushing or bypassing branch protection. Use when opening, updating, triaging red CI on, or landing an agent-authored GitHub PR. NOT for this repo's internal release ceremony, actor embodiments, or contributor mirror-sync mechanics (use port-daddy-internal-dev), tracking backlog/issue lifecycle across a board (use agent-issue-tracker-workflow), or deciding what to build next / sequencing a roadmap (use legible-roadmap-with-sidequests).

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Audit a compliance-ladder design (C0-C6) and transcript-fidelity ladder (T0-T5) plus their adapter conformance fixtures — Codex, Claude Code, Cloudflare, Ollama/LM Studio, custom stdio/HTTP agents — for the two failure modes that make a C-badge or T-fidelity label a lie: the ladder disagreeing with itself across doc/schema/ui/probe surfaces, and a level being reachable by self-report because no daemon-witnessed negative probe actually tries to forge it. Use when designing or freezing a compliance ladder, wiring an adapter conformance probe suite, deciding whether a numeric C-badge or T-label is safe to ship, or investigating a self-attestation or observed-to-controlled bypass risk. NOT for auditing a cryptographic protocol or whitepaper for adversarial soundness (`redteam-review`), writing TLA+/formal invariants for a daemon monitor (`runtime-verification-for-agents`), or agent identity, successor linkage, and reputation across restarts (`agent-identity-continuity-reputation`).

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Analyze a Coval adversarial / red-team testing report and turn it into an agent-hardening plan. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or a per-scenario scorecard from an adversarial sweep and wants evidence-backed next steps such as prompt/guardrail changes, refusal hardening, verification fixes, escalation routing, or expanded attack coverage.

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Analyze a Coval audio-quality testing report from runs across different voice, speaking-style, volume, interruption, and background-noise scenarios. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or metric summary and wants evidence-backed next steps such as prompt changes, tool handling fixes, STT/TTS adjustments, trace setup, or expanded audio-scenario coverage.

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Trial protocol for teaching AI Matrx an expert's knowledge until the platform breaks, fixing it. Use when asked to run an expertise trial, distil a person/creator/recent video into a Masterwork, or test the capture product. NOT for a known-missing feature (use build-sub-feature).

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.