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。
peacezha/TRACE☆ 32026年10月13日 更新
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。
peacezha/TRACE☆ 32026年10月13日 更新
Query and interpret security logs you are authorized to read. Build detections and investigations without leaking PII.
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。
lgzarturo/springboot-course☆ 32026年10月12日 更新
Agente que simula Bill Gates — cofundador da Microsoft, arquiteto da industria de software comercial, estrategista tecnologico global, investidor sistemico e filantropo baseado em dados.
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。
phoroth/AGENTIC☆ 32026年8月8日 更新
Systematically evaluate weak, stale, or low-conviction theses for upgrade, monitoring, or closure. Use when user says "prune", "kill list", "clean up theses", "what should I close", or "reduce portfolio".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Audit whether a thesis's stated conviction matches its evidence, and whether any Conviction Trigger has silently fired without being actioned. Use when user says "conviction audit", "is my conviction right on [TICKER]", "did a trigger fire", or "should I re-rate [TICKER]".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Extract and maintain a cross-portfolio catalyst calendar from all thesis notes. Use when user says "catalyst", "calendar", "what's coming up", "upcoming events", or "what could move the portfolio".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Extract a thesis's dependency fingerprint — the external variables its bull case actually rests on (key customers, suppliers/inputs, technology transitions, macro drivers, single points of failure). Use when user says "dependency map", "what does [TICKER] depend on", "dependency fingerprint", or "map exposures for [TICKER]".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Targeted deep research to fill a specific gap in an existing thesis. Use when user says "deepen", "flesh out", "expand on", "fill in", or specifies a thesis section to improve. Also supports --sync-metrics mode — detects stale financial metrics across every in-scope analytical section of a thesis (not just Key Metrics or Summary) and coherently updates every sentence that depends on them, using a Key-Metrics-table / FMP / web-search waterfall. Use when user says "sync metrics", "update the numbers throughout the note", or "fix stale figures across the whole thesis". The batch form `--sync-metrics --all-flagged` syncs every thesis flagged by the latest `/numbers --all-open` in one operation — detection fanned out to capped READ-ONLY agents, one consolidated confirmation gate, direct sequential writes (agents never write).
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Surface new insights, potential trades, and research opportunities from existing vault content. Use when user says "surface", "what am I missing", "find opportunities", or "what should I research next".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Refresh the Key Metrics table in a thesis with current data from Financial Modeling Prep, with a scoped web-search fallback (Step 4b) when FMP has no data or resolved the wrong company. Use when user says "numbers", "refresh metrics", "update key metrics", or "refresh [TICKER]" with no other action implied. Surgical edit only — does NOT create research notes or propagate via $sync. Also flags (never auto-edits) stale price/valuation framing in the thesis Summary — see Step 10b.
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Restore a thesis, sector, or macro note from a snapshot in _Archive/Snapshots/. Use when user says "rollback", "restore", "revert", "undo sync", or "go back to the previous version".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Run health checks on the vault for inconsistencies, stale data, orphaned notes, and missing connections. Use periodically or when user says "lint", "health check", or "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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Earnings-season triage across ALL active theses (not just Live Portfolio holdings) — every earnings call reported inside the window gets a Quartr event summary, a Conviction-Trigger/Outstanding-Questions cross-reference, and a coverage check against existing Research notes, producing a ranked deep-read queue for /transcript. Use when user says "earnings sweep", "who reported", "triage earnings", "catch up on earnings season", or after any earnings-heavy stretch. Default window 14 days; `/earnings-sweep 90` covers a full season.
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Delete old snapshots from _Archive/Snapshots/. Accepts a day threshold (default 180). Also `daily-intel [days]` mode — prune auto-generated n8n scanning surfaces (news briefs, X dashboards) from Daily Intel/ older than 90 days. Use when user says "clean", "clean snapshots", "delete old snapshots", "clean daily intel", or when /lint flags stale snapshots.
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Generate a backward-looking retrospective of vault activity (addressed callouts + Log entries) over a time window (1w / 1m / 1q), overlay with newsflow + earnings transcripts + price action, and rank trade ideas by the gap between official narrative and market reaction. Output is an immutable Research note. Use when user says "retro", "retrospective", "what did I do this week/month/quarter", "review activity against market", or "recommend trades from recent research".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Map a thesis's position in its value chain — who it buys from, sells to, and competes with; where the bottleneck and pricing power sit; and whether it owns a critical layer. Use when user says "value chain", "supply chain position", "where does [TICKER] sit", or "who are [TICKER]'s suppliers/customers".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Pull an earnings call transcript from Financial Modeling Prep, extract qualitative signal (management commentary deltas, hedging shifts, Q&A tone), and produce a thesis-delta-first Research note. Use when user says "transcript", "pull earnings call", "transcript diff", or "ingest [TICKER] earnings".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Side-by-side competitive comparison of two or more companies. Use when user says "compare", "X vs Y", "which is better", or asks about competitive dynamics between specific companies.
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Change conviction level or status on a single thesis. Use when user says "change conviction", "downgrade", "upgrade", "move to monitoring", "close [TICKER]", or "set [TICKER] to [level]".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Export/publish the live portfolio tracker as a static, stripped snapshot into the "Portfolio Snapshot" folder — an empty Trades section (first), the holdings table, and the 1-month-return bar chart baked to static SVG (scatter chart opt-in), with a Publish_Snapshot property. Strips all instruction/engine/log elements (refresh dataviewjs, tip callouts, Upcoming Earnings, Column Legend, Notes, Log). Use when the user says "snapshot the portfolio", "publish the portfolio", "export Live Portfolio", or "portfolio snapshot".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Extract a thesis's load-bearing assumptions and scan for internal contradictions — the falsifiable claims the bull case requires, what would falsify each, and where the thesis's own Risks / Bear Case / research already argue against it. Use when user says "assumptions", "what must be true", "load-bearing assumptions", or "does [TICKER] contradict itself".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新
Adversarial thesis testing — act as a short seller to find the weakest points in a thesis. Use when user says "stress test", "devil's advocate", "challenge this thesis", or "break [TICKER]".
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。
jameswong2011/InvestmentVault☆ 32026年9月9日 更新