「recon」の検索結果

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。

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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 the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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。

Reconstruct workflow behind a past coding-agent artifact using local ax sessions/commits/skills/tool traces. Use when asked how X was built.

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。

Conviction-trigger surveillance via Quartr keyword alerts — parse every active thesis's Conviction Triggers for named observables, propose keyword alerts scoped to the Vault Active watchlist (or market-wide for macro observables), create them ONLY on explicit user confirmation, and reconcile the alert set against the book as theses open/close. Use when user says "monitor", "set up alerts", "keyword alerts", "watch for X", or "reconcile alerts".

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。

Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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。

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。

Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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。

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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 network reconnaissance and port scanning using Suricata and Snort IDS signatures, threshold-based detection rules, and traffic anomaly analysis to identify Nmap, Masscan, and custom scanning activity.

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。

Parse Windows LNK shortcut files to extract target paths, timestamps, volume information, and machine identifiers for forensic timeline reconstruction.

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。

Wi-Fi reconnaissance methodology — adapter selection, monitor mode and packet injection setup, regulatory domain handling, multi-band airspace mapping, hidden SSID discovery, BSSID/ESSID/channel/PMF/encryption fingerprinting, client probe analysis, vendor OUI lookup, war-driving with Kismet/airodump-ng/Wigle, and structured airspace data capture for downstream attacks. Use at the start of any wireless engagement to build the target map before active attacks; covers 2.4 GHz, 5 GHz, and 6 GHz (Wi-Fi 6E) bands and adapter compatibility for each.

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。

Discover a single-page-app's hidden backend API from its public JS bundle, then test that API for broken access control / missing authentication. One of the highest-yield web plays in modern recon — SPAs ship their entire backend route map to the browser, and the API behind them is frequently missing the auth middleware the login page implies. Built from an authorized engagement where this play found an unauthenticated financial API that an ASM scan reporting hundreds of 'Criticals' completely missed. Use whenever a target serves a JS-heavy SPA (React/Vue/Angular/Next), an 'app'/'console'/'dashboard'/'portal' subdomain, or any `*api*` host shows up in recon. Leaked build artifacts (source maps / .env / .git / asset-manifest) are owned by hunt-source-leak; API version-inventory and behavioral diffing by hunt-shadow-api; this skill owns mapping a live SPA's backend routes from its JS bundle and testing them for broken access control / missing auth.

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。

You are helping a penetration tester perform network reconnaissance and service

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。

Advanced CV for infrastructure inspection including forest fire detection, wildfire precondition assessment, roof inspection, hail damage analysis, thermal imaging, and 3D Gaussian Splatting reconstruction. Expert in multi-modal detection, insurance risk modeling, and reinsurance data pipelines. Activate on "fire detection", "wildfire risk", "roof inspection", "hail damage", "thermal analysis", "Gaussian Splatting", "3DGS", "insurance inspection", "defensible space", "property assessment", "catastrophe modeling", "NDVI", "fuel load". NOT for general drone flight control, SLAM, path planning, or sensor fusion (use drone-cv-expert), GPU shader development (use metal-shader-expert), or generic object detection without inspection context (use clip-aware-embeddings).

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。

Designs or reviews provenance-bound DAG attempt traces, coverage gaps, cancellation, and unknown-effect reconciliation. NOT for claiming execution completeness, deployment monitoring, or root-cause proof.

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 for bounded reasoning, partial planning, commitment policy, deliberation cost, and reconsideration-threshold design instead of assuming free deliberation. NOT for exhaustive planning, static optimization, or domains where reconsideration cost is irrelevant.

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。

Run the ECC engineering process retroactively against an existing project slice. Audit current state, reconstruct past decisions, produce a four-axis gap register (thinking, coding practice, missing features, technology selection), then execute fixes forward through the plan-TDD-review pipeline. Use when adopting ECC mid-project, taking over an inherited codebase, or asking what was missed and what would have been built differently from day one.

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。

複数回のインタビューでブランドの目的、顧客像、個性、語り口を掘り下げ、創業者間の認識の違いも整理して、協力者に共有できるブランドブックにまとめます。

• 新ブランドの方向性を決めたいとき
• ブランドの立ち位置を見直したいとき
• 複数の創業者の認識をそろえたいとき

ECCの導入・更新・再設定を、利用中のエージェント環境に合わせて進めます。導入状況の確認から変更内容のプレビュー、適用、検証までを対話形式で案内します。

• ECCを導入・更新したいとき
• Claude Codeで導入範囲を移したいとき
• Claude Codeでフックを調整したいとき

許可されたWebアプリを対象に、公開ページの調査から脆弱性の再現確認まで進め、証拠・影響・修正案をまとめたセキュリティ報告書を作るスキル。

• ステージングの脆弱性を調べたいとき
• 疑わしい脆弱性を再現確認したいとき
• 証拠と修正案を報告書にまとめたいとき

ドメインのサブドメイン、SSL証明書、登録情報、DNSレコードを調べるスキル。複数ドメインの一括調査や登録状況の推定に対応し、結果をJSONで返します。

• 公開ログからサブドメインを探したいとき
• SSL証明書の期限を確認したいとき
• 登録情報やDNS設定を調べたいとき

言語モデル内部の反応を少数の特徴に分解し、学習した概念を調べます。学習済みSAEの分析、自作SAEの訓練、特徴を使った出力調整と品質評価を案内します。

• 学習済みSAEで特徴を調べたいとき
• 特定のモデル層にSAEを訓練する
• 入力文ごとの特徴の反応を比較する