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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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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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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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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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The frontend Error Inspector capture system (captureError, lib/diagnostics/**). Use when wiring a new CapturedErrorSource or adapter, calling captureError from a new site, picking a red/orange/yellow tier or errorTierRules downgrade, or turning a console.error or swallowed catch into a captured error.

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opencode CLIの動作確認を行うシンプルなスキル。 インストール状態、runコマンド、モデル応答の3項目をチェックする。 Trigger: opencode動作確認, opencode check, opencodeが動くか確認

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Находит точную причину повторного падения процессов сервера 1С в Linux: SIGABRT, технологический журнал, core dump, GDB, C++-исключения и проверка причины. Используйте, когда rphost, ragent или rmngr исчезает, становится zombie, завершается сигналом 6 или оставляет core.

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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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Complete guide for xUnit test output and logging. Use when you need to implement test output, diagnostic logging, or ILogger alternatives in xUnit tests. Covers ITestOutputHelper injection, AbstractLogger pattern, structured output design. Includes XUnitLogger, CompositeLogger, performance test diagnostic tool implementations. Keywords: ITestOutputHelper, ILogger testing, test output xunit, test output, test logging, AbstractLogger, XUnitLogger, CompositeLogger, testOutputHelper.WriteLine, test diagnostics, logger mock, test log, structured output, Received().Log

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Single entry point for all AEM as a Cloud Service Workflow skills. Covers workflow model design, custom process step and participant chooser development, launcher configuration, workflow triggering, and production support including debugging stuck/failed workflows, triaging incidents with Cloud Manager logs, thread pool analysis, and Sling Job diagnostics for the Granite Workflow Engine.

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Creates comprehensive GitHub Actions CI/CD workflows for linting, testing, building, and deploying. Includes caching strategies, matrix builds, artifact handling, and failure diagnostics. Use for "GitHub Actions", "CI pipeline", "workflow automation", or "continuous integration".

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Analyze Clawdbot logs and diagnostics. Use when the user asks about bot performance, response times, errors, session stats, token usage, API costs, or wants to debug slow responses.

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