433건 · 관련도순
Diagnose Azure application and infrastructure issues with a structured, evidence-based workflow. Use this skill when users ask to troubleshoot outages, latency, failures, configuration drift, or anomalies. Root cause analysis using logs, metrics, traces, and dependency mapping.
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Build and diagnose visionOS projects with Seiro MCP. Use inspect_xcode_schemes (if needed) -> validate_sandbox_policy -> build_visionos_app -> inspect_build_diagnostics (on failure) -> fetch_build_output (on success), and avoid direct xcodebuild or swiftc unless the user explicitly asks for shell-level execution or MCP cannot handle the task.
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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.
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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.
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Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling, and LD-aware regional rendering. Use when visualizing association results across the genome, comparing two traits, computing genomic inflation lambda, or zooming into a locus with LD coloring.
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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.
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Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.
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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.
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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.
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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.
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Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing risks via Fine-Gray vs cause-specific Cox, weighted log-rank and MaxCombo for non-proportional hazards, recurrent events (Andersen-Gill, PWP, WLW), and interval-censored data. Use when analyzing time-to-event endpoints (OS, PFS, DOR, TTR, TTNT) in oncology or other clinical trials.
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Use when a network probe, DNS lookup, HTTP fetch, or nmap scan reports the target host or the internet is unreachable. Stops further probing and reports a target-readiness blocker with useful diagnostics.
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Forensic root cause analyzer for Antigravity sessions. Classifies scope deltas, rework patterns, root causes, hotspots, and auto-improves prompts/health.
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Add useful diagnostics, choose log levels, preserve context, and handle player-facing failures safely.
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Create or repair a project-local Inspector profile after INSPECTOR_PROFILE_REQUIRED, INSPECTOR_PROFILE_INCOMPLETE, INSPECTOR_PROFILE_INVALID, or PROFILE_AUTHORING_REQUIRED, using Unity component source, custom Inspector evidence, serialized surfaces, and validation diagnostics.
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Use when writing, reviewing, restoring, trimming, or auditing prose in the deepseek-harness repo, including deciding where documentation or comments are required across Markdown, JSDoc, code and test comments, prompts, descriptions, diagnostics, and CLI or UI strings.
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Use when a HyperFrames composition needs a punch-in, punch-out, zoom, reframe, Ken Burns treatment, camera move, visual match/whip handoff, or other seek-safe 2D/3D keyframes; also for GSAP, CSS keyframes, Anime.js, WAAPI, FLIP, paths, masks, SVG morph/draw, text trails, 3D depth, or `hyperframes keyframes` diagnostics. Don't use for broad scene strategy, brand design, media sourcing, captions, or general video planning.
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Use when shared-IP HTTPS hosts serve the wrong application only on reused HTTP/2 connections—map DNS, SAN, SNI, :authority, listener, and backend ownership before applying 421.
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Use when a SQLite database in WAL mode has a growing -wal file, repeated incomplete checkpoints, SQLITE_BUSY, disk-pressure risk, or reader slowdowns that may indicate checkpoint starvation.
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Reviews and fixes Swift concurrency: Swift 6 strict-concurrency compiler errors, Sendable conformance, actor isolation, @MainActor, and data-race safety. Use when migrating async code to Swift 6 or resolving concurrency diagnostics.
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Use when diagnosing agent benchmarks or runtime failures from trajectories instead of aggregate pass rates. Builds shared action-observation decision landscapes, identifies productive cores and trap regions, profiles Access/Trap/Repair behavior, and designs conservative trap-triggered recovery experiments.
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Foundational ethics, authority hierarchy, and structural principles for the Predicate agent. Always-on law (composable system-prompt core): Truth>Harmony, Evidence>Authority, Halt>Assumption, Outcomes>Process — four ordered principles that govern every walk. Reference (by-moment): conflict resolution, ethics adjudication, novel situations, precedence walkthrough, entropy diagnostics, principled resistance. Trigger (reference depth): resolving rule conflicts, ethics calls, novel situations. Prompt contains: constitution, principles, precedence, truth over harmony, outcomes over process, evidence over authority, principled resistance.
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The case-law chronicle of this repo's major failures — symptom, root cause, evidence, status, and the rule each battle minted — so nobody re-fights a settled battle or re-proposes a rejected fix. Use when a bug/incident looks familiar ("didn't this happen before?"), when you're about to propose an approach that may have been tried and rejected (e.g. shipping a migration from a package), when someone asks "why does rule X exist" / "why is done-by-lgtm a thing" / "what was incident 988", or when a bug-archaeology run hits the shallow-clone wall and needs the pre-June-2026 history. Trigger phrases: "has this broken before", "why can't packages ship migrations", "why did graduation fail", "why is the green-build lesson a rule", "what did we learn from incident NN". (For a live "build is green but the app is broken" symptom, start at crouton-diagnostics-index. NB keep this description free of any space-then-hash sequence — an unquoted YAML scalar treats space-hash as a comment start and silently truncates.)
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Recreate the nuxt-crouton dev environment from scratch and survive its install/build traps — the pnpm toolchain, the cold-start sequence (why packages must build before apps prepare), the version catalog and workaround pins, the per-app typecheck rule, required env vars, and the known environment traps. Use when setting up a fresh clone/worktree, when "pnpm install" or "nuxt prepare" fails, when an app won't boot after install, when typecheck output looks insane, or when a tool "isn't available". Trigger phrases: "set up the repo from scratch", "why does typecheck show thousands of errors", "playwright install fails", "what pnpm/node version". (Exact error strings — "Could not load '@fyit/crouton-*'", "Cannot find module '@vue/compiler-sfc'" — route via crouton-diagnostics-index first; it points back here for depth.)
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