「stable」の検索結果

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。

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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。

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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。

Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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。

Shared vocabulary for designing deep modules. Use when the user wants to design or improve a module's interface, find deepening opportunities, decide where a seam goes, make code more testable or AI-navigable, or when another skill needs the deep-module vocabulary.

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。

Master of defensive Bash scripting for production automation, CI/CD pipelines, and system utilities. Expert in safe, portable, and testable shell scripts.

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。

Master proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design to build maintainable, testable, and scalable systems.

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。

CI環境で安定動作するPythonテスト（特にstructlogのログ検証）を書く際に使用。「CIで失敗する」「capture_logsが不安定」「ログアサーションがCIだけ落ちる」「caplogフォールバック」「ANSI混入」「xdistでログが取れない」という課題で起動。capture_logs→caplogフォールバック→ANSI正規化→アサーション設計の流れで堅牢なテストを書く。

Independent, traceable code review of one SDD Composy task in review_required against its approved PRD, stories, TechSpec, evidence, and project rules, with stable findings and severities. Use when a task passed QA and evidence — 'revisar a TASK-003', 'code review da task', 'review this task's diff'. Do NOT use for code review outside an SDD workspace (use the host code review), for QA (sdd-qa), or for verification (sdd-verify).

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。

Create or revise the problem-first SDD Composy PRD (tasks/prd-SLUG/prd.md) with stable RF/CA identifiers, stopping at the human approval gate. Use when a user problem needs a product contract — 'criar o PRD', 'documento de requisitos', 'revisar o PRD do slug X', 'write the requirements for…'. Do NOT use for user stories (sdd-stories), technical design (sdd-techspec), or PRDs outside an initialized SDD workspace.

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 code review of an explicit range or set of files — correctness, security, performance, conventions, tests — with stable findings (CR-nnn, BLOCKER..INFO) and rule citations — 'revisar os últimos commits', 'code review da feature X', 'review base..HEAD'. Plans a REPORT-mode review (no code changes, no commit). Do NOT use to fix code (feat-feature / feat-quick), to write tests (feat-test) or for UI/UX design critique.

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。

Find deepening opportunities in a codebase, informed by the domain language in CONTEXT.md and the decisions in docs/adr/. Use when the user wants to improve architecture, find refactoring opportunities, consolidate tightly-coupled modules, or make a codebase more testable and AI-navigable.

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 authoritative, deterministic, weighted, and testable randomness without breaking prediction or reproducibility.

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。

Decompose multi-step work into a revisable subgoal plan with stable step IDs, checkpointing, and plan-ahead execution. Load when a task needs explicit planning before action, subgoal decomposition, plan checkpointing, or ReCAP-style plan-ahead execution. Also triggers on "structured plan", "plan with steps", "subgoal graph", "revise the plan", "checkpoint plan", or multi-step tasks where naive one-shot execution would be fragile. Skips trivial single-step tasks. Pairs with dynamic-routing on failure. Distinct from process-decomposer (registry/triage) and problem-to-plan (doc deliverables).

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。

Promote project-specific memories into strict, small global memory only when they are cross-project, stable, useful, safe, and worth the global context cost. Load when the user says make this global, remember across projects, save this globally, or promote this learning.

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。

Mirror issues and status across issue trackers with stable external-ID mapping to avoid duplicates. Load when syncing GitHub and Linear issues, mirroring ticket status, or keeping two trackers in sync. Also triggers on "issue sync", "sync issues", "mirror issues to", "keep Linear and GitHub in sync", or bidirectional issue tracker updates. Requires API access on both sides — stops if credentials missing.

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。

Design stable APIs and module boundaries — contract-first types, consistent errors, boundary validation, additive changes. Load when designing REST or GraphQL endpoints, public module interfaces, component props, or FE/BE contracts. Also triggers on "API design", "interface design", "design the API", "module boundary", "API contract", "define the interface". Complements feature-spec (product layer). Routes breaking retirement to api-deprecation-and-migration when it exists.

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。

Master of defensive Bash scripting for production automation, CI/CD pipelines, and system utilities. Expert in safe, portable, and testable shell scripts.

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。

Master proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design to build maintainable, testable, and scalable systems.

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。

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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。

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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。

Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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。

Compare before/after Coval runs using matched cases, stable metric versions and inspected conversation evidence. Use to assess a regression or proposed improvement; does not automatically launch or tune anything.

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。