「coverage」の検索結果

Review requirements, coverage, results, evidence, and findings without changing the product or recorded state.

日本語の概要は準備中です。原文の説明を表示しています。

Execute an explicitly authorized exploratory charter and record notes, findings, evidence, and follow-up without claiming false coverage.

日本語の概要は準備中です。原文の説明を表示しています。

Use when the user wants tests planned for existing code or a test audit — unit, integration, E2E scenarios exportable to Playwright, playwright-cli UI checks, a coverage matrix — 'criar testes para o UserService', 'plano de testes E2E do login', 'auditar a cobertura'. Writes .planning/feat/features/{slug}/plan.md. Do NOT use for code review (feat-review), for implementing features (feat-feature) or to run an existing plan (feat-exec).

日本語の概要は準備中です。原文の説明を表示しています。

Use when the user wants a UI-only action plan — components, pages, composables/hooks, state, forms and their E2E coverage — 'plano de frontend para a tela X', 'plan the settings page'. Writes .planning/feat/features/{slug}/plan.md with E2E scenarios and playwright-cli checks. Do NOT use for API/database work (feat-backend), full features (feat-feature), writing code (feat-exec) or UI review (feat-review).

日本語の概要は準備中です。原文の説明を表示しています。

Review a code diff or explicit file set through independent correctness and QA lenses. Use when the user asks for a code review, test-coverage assessment, pre-merge audit, or review gate in a PWDEV Flow workflow.

日本語の概要は準備中です。原文の説明を表示しています。

Improve code structure, readability, and maintainability without changing external behavior through systematic refactoring techniques like extracting functions, removing duplication, simplifying conditionals, and applying design patterns. Use when reducing technical debt, extracting functions or classes, removing code duplication, simplifying complex conditionals, renaming for clarity, applying design patterns, improving code organization, reducing coupling, increasing cohesion, or maintaining test coverage during structural improvements.

日本語の概要は準備中です。原文の説明を表示しています。

Systematically review pull requests, feature implementations, and code changes to ensure quality, maintainability, security, and adherence to best practices. Use when reviewing code before merging, conducting peer reviews, performing self-reviews, auditing code quality, checking for security vulnerabilities, ensuring consistent coding standards, verifying test coverage, assessing performance implications, evaluating architectural decisions, or providing constructive feedback to improve team code quality.

日本語の概要は準備中です。原文の説明を表示しています。

Three-axis orchestrator: (1) clean section boundaries — naming, routes, views, ViewModels, DB ownership, cross-section access; (2) internal cohesion — no EF in service layer, caching in service only, proper interfaces, reusable ViewComponents, architecture-test coverage; (3) focused tests — grouped under the section, covering invariants/negatives/triggers, pruned of redundancy. Push-and-bot-review loop. Use when a sizable PR landed, a section shows arch drift, or /pr-review returned a non-trivial violation list. Camps is the gold-standard reference.

日本語の概要は準備中です。原文の説明を表示しています。

Stryker-driven test cull: delete slop, consolidate redundants, fill mutation-coverage gaps. Score up, test count and lines down. Use when the user says 'trim tests', '/trim-tests', or wants to clean up LLM-generated test bloat. No args picks the worst-scored file; argument scopes to a section, service, or file.

日本語の概要は準備中です。原文の説明を表示しています。

Eng manager-mode plan review. Lock in the execution plan — architecture, data flow, diagrams, edge cases, test coverage, performance. Walks through issues interactively with opinionated recommendations. Use when asked to "review the architecture", "engineering review", or "lock in the plan". Proactively suggest when the user has a plan or design doc and is about to start coding — to catch architecture issues before implementation. (gstack) Voice triggers (speech-to-text aliases): "tech review", "technical review", "plan engineering review".

日本語の概要は準備中です。原文の説明を表示しています。

Generate and run tests for Adobe App Builder actions and UI components. Scaffolds Jest unit tests, integration tests against deployed actions, contract tests for Adobe API interactions, and React component tests using Testing Library. Provides mock helpers for State, Files, Events SDKs, @adobe/aio-lib-* clients, ExC Shell context (@adobe/exc-app), and UIX Guest SDK (@adobe/uix-guest). Use this skill whenever the user mentions testing App Builder actions, writing unit tests for Runtime actions, creating integration tests, mocking Adobe SDKs, setting up test fixtures, running aio app test, or wants to verify action behavior before deployment. Also trigger when users mention Jest configuration for App Builder, test coverage, CI test setup, React component test, Testing Library, UI test, Provider wrapper, test my page, test my form, test my table, test my component, mock shell context, mock extension context, debug test failures, or fix Jest errors.

日本語の概要は準備中です。原文の説明を表示しています。

Validate, migrate, and atomically persist files and configuration with safe fallback and restart coverage.

日本語の概要は準備中です。原文の説明を表示しています。

Reproduce failures, trace authoritative flow, prove the broken assumption, and add targeted regression coverage.

日本語の概要は準備中です。原文の説明を表示しています。

Implement minimal network events and component state with authority, conversion, dirtying, and regression coverage.

日本語の概要は準備中です。原文の説明を表示しています。

Detect and resolve naming collisions, overlapping intent triggers, and insufficient intent diversity across the skill library. Load when a new skill is created (called by universal-skill-creator), during improvement passes (called by improve-skills), or when the user asks to deconflict skills, check for naming collisions, audit trigger overlap, review intent coverage, find duplicate triggers, check skill names, or says "are any skills too similar", "which skills overlap", "deconflict the library", "check for confusing skill names", "intent audit".

日本語の概要は準備中です。原文の説明を表示しています。

Review a built frontend against its chosen direction, catch drift back to generic AI defaults, enforce state coverage, ethical patterns, UX heuristics, and polish, and check contrast with APCA (not the legacy WCAG ratio). Produces specific, prioritized fixes — never vibes-based feedback. Works with pasted screenshots or Playwright MCP automated capture. Load when the user asks to review a UI, audit a design, check if a frontend looks generic or vibecoded, evaluate visual quality or polish, says "review this UI", "is this design good", "audit my frontend", "does this feel like [product]", "design QA", or when frontend-design routes here. Sub-skill of frontend-design.

日本語の概要は準備中です。原文の説明を表示しています。

Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

日本語の概要は準備中です。原文の説明を表示しています。

Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

日本語の概要は準備中です。原文の説明を表示しています。

Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

日本語の概要は準備中です。原文の説明を表示しています。

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

日本語の概要は準備中です。原文の説明を表示しています。

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

日本語の概要は準備中です。原文の説明を表示しています。

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.

日本語の概要は準備中です。原文の説明を表示しています。

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

日本語の概要は準備中です。原文の説明を表示しています。

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

日本語の概要は準備中です。原文の説明を表示しています。