「c2」の検索結果

Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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。

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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。

Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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。

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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。

ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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。

Map controls to SOC2, ISO 27001, PCI, or internal policy for the org you work for. Evidence and control design — not audit theater.

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。

Uncorrelated Evaluator — 4軸ルーブリック専門エージェント（functionality-reviewer・code-reviewer・design-reviewer・originality-reviewer）と security-reviewer を5並列実行し、成果物を多面的に独立評価します。PASS / NEEDS WORK / BLOCKED 判定を返します。Self-leniency 防止のため、実装エージェントのコンテキストを引き継がない新規エージェントとして起動します。「レビューして」「評価して」「実装を確認して」などのリクエストで起動します。

フレーキーテスト（不安定なテスト）を検出・分類・修正支援するスキル。 以下のような状況で使う： - 「テストが時々失敗する」「CI が時々落ちる」 - 「同じコードなのにテスト結果が変わる」 - 「flaky test」「不確定」「再実行すると通る」 - 「テストが不安定」「テストの信頼性が低い」 t-wada式TDDの信頼性基盤を守るために使用する。 引数で実行回数を指定可能（デフォルト: 5回）。

テストカバレッジのギャップを体系的に分析し、実際に動くテストコードを提案するスキル。 以下のようなときに使う： - テストカバレッジを改善したい・不足テストを特定したい - 「テストが足りない」「カバレッジを上げたい」「どこをテストすべき」 - 「未テストの関数」「what tests am I missing」「improve test coverage」「coverage gap」 t-wada式TDDの原則に基づき、テストの抜け漏れを特定して優先度付きで補完する。 引数: 分析対象ファイル・ディレクトリ（省略時はプロジェクト全体）

features.json を読み込み、pending な機能を1件ずつ tdd-guide エージェント（内部で tdd-cycle を使用）で実装するスキル。 Context anxiety（トークン上限接近による焦り）と Context rot（情報劣化）を防ぐため、 機能単位のループ・状態管理・implementation-notes.md への記録を担う。 builder エージェントが実装フェーズを開始するときは必ずこのスキルを呼ぶ。

任意のタスク（GitHub Issue・自由記述リクエスト・口頭要件）を起点に、受け入れ条件確認・スコープ定義・影響分析・テスト戦略を含む実装計画（15セクション）と、builder エージェントへ渡す features.json を生成します。「〇〇を作って」「実装計画を作って」「Issue

t-wada式TDD（テスト駆動開発）でRED→GREEN→REFACTORサイクルを使ってテストファーストで開発を進めるスキル。 ユーザーが「TDDで実装して」「テストファーストで」「t-wada式で」「REDから始めて」「失敗するテストを先に」と言った場合は必ずこのスキルを使うこと。 FizzBuzz、スタック、認証、バリデーションなど、あらゆる実装タスクにTDDアプローチを適用できる。 ユーザーが実装を始めようとしているときは積極的にTDDを提案すること。

Iteratively detects and auto-fixes technical debt in a codebase using three quality criteria from debt-analysis references: conditional branch simplification, encapsulation, and separation of concerns. Applies fixes directly to code, runs existing tests to verify no regressions, re-analyzes, and loops until all high-severity issues are resolved or max iterations (5) reached. Use this skill when you want to automatically improve code quality with real code changes, reduce technical debt systematically, or clean up code to meet quality standards. Trigger on phrases like "fix technical debt", "clean up code quality", "refactor and fix issues", "improve code quality automatically", "apply debt fixes", "fix code problems", "eliminate debt".

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。

Planner→Builder→EvaluatorのLong-Runningエージェントハーネスで複雑なタスクを実装します。plannerがfeatures.jsonに機能を分解し、builderがTDDで1機能ずつ実装し、evaluatorがPASSするまでbuilderを繰り返します。「〇〇を作って」「実装して」「long-running」などのリクエストで起動します。

Arquitetura e diagnóstico AWS — VPC, EC2, ECS, EKS, ALB, NLB, RDS, ElastiCache, S3, CloudFront, Route53, IAM, WAF, GuardDuty. Use quando o usuário disser "AWS", "VPC", "ALB", "RDS", "revisar a arquitetura", "Well-Architected", "subnet", "security group", "IAM", ou citar qualquer serviço AWS. Leitura livre; qualquer mudança passa pelo portão de confirmação.

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。

Analisa custo AWS e identifica desperdício em EC2, RDS, S3, EKS, EBS, Elastic IP, NAT Gateway e tráfego. Use quando o usuário disser "custo", "fatura", "está caro", "FinOps", "reduzir gasto AWS", "Cost Explorer", "otimizar custo". Quase todo leitura — seguro por natureza.

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 II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-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。

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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。

Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling 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。

Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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。

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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。

Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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。

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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。

ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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。