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概要と使いどころ
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
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Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before statistical analysis.
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Use when deciding whether a microeconomics project fits the American Economic Journal: Microeconomics (AEJ: Micro) rather than JET, GEB, Theoretical Economics, Econometrica, or AEJ: Applied. Tests scope and broad-interest fit; it does not develop the model (see aejmic-theory-model).
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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.
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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.
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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.
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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.
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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.
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Query Metabolomics Workbench for metabolomics study data
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Channel economics: design and analyze the financial structure of go-to-market channels. Use when picking a channel mix, modeling partner margin or TCO, designing partner tiers and rebates, or analyzing channel conflict.
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omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existin
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Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
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Multi-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi-omics. MuData holds per-modality AnnData with shared obs. WNN joint embedding, per-modality preprocessing, MOFA factor analysis. Use scanpy-scrna-seq for single-modality RNA; use muon when combining 2+ omics from the same cells.
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MS data processing with PyOpenMS for LC-MS/MS proteomics and metabolomics — mzML/mzXML I/O, signal processing (smoothing, peak picking, centroiding), feature detection/linking, peptide/protein ID with FDR, untargeted metabolomics. Use matchms for simple spectral matching.
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Think and work like an expert Metabolomics Scientist. Use when a task calls for Metabolomics Scientist judgment. Reasons from MSI annotation levels, pooled-QC RSD and D-ratio gates, MZmine/MS-DIAL/XCMS pipelines, HMDB/GNPS identification, and MetaboAnalyst batch correction (ComBat, QC-RLSC); treats injection-order drift, ComBat over-correction, and Level-5 pathway stories as first-class failure modes.
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Think and work like an expert Functional Genomics Scientist. Use when a task calls for Functional Genomics Scientist judgment. Reasons from perturbation as causal probe, genotype-to-phenotype linkage, library representation, and effect-size-plus-FDR statistics through MAGeCK/BAGEL/CERES-Chronos, CRISPRcleanR, CRISPResso2, MPRAnalyze, and Perturb-seq pipelines while treating MOI/bottleneck artifacts, copy-number and p53/DSB toxicity, RNAi seed effects, and guide-assignment or gating errors as first-class failure modes.
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Think and work like an expert Connectomics Scientist. Use when a task calls for Connectomics Scientist judgment. Reasons from vEM acquisition and petascale alignment through FFN/RoboEM segmentation, FlyWire/neuPrint/MICrONS/H01 graphs, and synapse-level QC while treating split/merge errors, alignment tears, false synapses, and release-version drift as first-class failure modes.
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Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.
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Detects circadian and ultradian rhythms in time-series omics data using CosinorPy cosinor models, MetaCycle (JTK_CYCLE, ARSER), and RAIN non-parametric tests. Fits cosine models to estimate phase and amplitude, tests rhythmicity significance at pre-specified periods. Use when testing for 24-hour or other known-period oscillations in circadian, feeding-fasting, or light-dark cycle experiments. Not for unknown-period discovery (see temporal-genomics/periodicity-detection).
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Understand essential business finance — profit margins, unit economics, cash flow, LTV/CAC, and the 4 methods to increase revenue. Use when: analyzing business profitability, making pricing decisions, evaluating SaaS unit economics, financial planning.
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加密链上交易 (加密 / 链上交易 (Crypto & On-chain Trading) — 以加密资产为标的、强调链上活动的主动交易认知操作系统：从「看叙事/选赛道 → 找标的 → 链上尽调与风控 → 选场所(DEX/CEX/链上合约) → 建仓与仓位管理 → 监控链上流向与情绪 → 退出与复盘」的完整决策链。覆盖 (a) 第一性张力 — **链上 on-chain (DEX 现货/AMM、钱包追踪 wallet tracking、资金流向 flow、MEV、memecoin、链上衍生品 Hyperliquid/GMX、自托管 self-custody, 'not your keys not your coins') ⇄ 链下 CEX (中心化交易所现货/合约 Binance/OKX/Bybit、订单簿、托管、出入金法币)**; **合约/杠杆/衍生品 (perps 永续、资金费率 funding、清算 liquidation、爆仓、做多做空、高频/择时) ⇄ 现货/价值/长持 (spot、HODL、定投 DCA、基本面/估值、'time in market > timing the market')**; **价值/基本面派 (协议收入、TVL、代币经济学 tokenomics、真实使用、估值模型) ⇄ meme/叙事/情绪派 (memecoin、narrative rotation 叙事轮动、attention is the asset、纯博弈/PvP、Ponzinomics)**; **链上数据/量化/客观 (on-chain analytics, Nansen/Arkham/Dune、聪明钱 smart money、链上指标、系统化/机械化) ⇄ 直觉/盘感/叙事阅读 (narrative、KOL alpha、社群情绪、tape reading)**; **自托管/去中心化/抗审查 (DeFi、自托管钱包、抗审查、'be your own bank') ⇄ 便利/合规/中心化 (CEX、合规出入金、KYC、托管、ETF)**; **主动交易/择时/高换手 (trading、波段、合约、撸毛/空投 airdrop farming、套利 arbitrage) ⇄ 被动配置/低换手 (配置 BTC/ETH、ETF、长期叙事 beta)**; (b) 核心工作流 / pipeline (最标准、最易蒸高质量 + CLI 化) — 通用链: 叙事/赛道判断 (宏观周期/减半/流动性/板块轮动) → 标的发现 (链上扫链/聪明钱跟单/新币/叙事映射) → 尽调 due diligence (代币经济学/解锁 unlock/团队/合约审计/honeypot 检测/流动性与持仓分布) → 风控前置 (仓位 sizing/最大回撤/止损/相关性) → 场所与执行 (CEX vs DEX、滑点/MEV/gas、限价 vs 市价、TWAP) → 持仓监控 (链上流向/巨鲸/资金费率/解锁日历/情绪指标) → 退出与复盘 (止盈分批/再平衡/记录交易日志); 子流派 SOP: 链上 degen 打新与 memecoin 流程、合约交易者的资金费率与清算地图、空投/撸毛 farming、套利与 MEV、被动配置与定投; (c) 工具栈 — 链上分析 (Nansen 聪明钱/Arkham 实体标注/Dune 自建仪表盘/Dexscreener & DEX Screener 新币/GMGN & Photon & BullX memecoin 终端/Etherscan & Solscan 区块浏览器/DeBank 钱包总览/Token Terminal 协议基本面/DefiLlama TVL/Glassnode & CryptoQuant 链上指标)、交易场所 (CEX: Binance/OKX/Bybit/Coinbase; 链上现货 DEX: Uniswap/Jupiter/Raydium/Aerodrome; 链上衍生品: Hyperliquid/GMX/dYdX)、钱包与安全 (MetaMask/Rabby/Phantom 热钱包、Ledger/Trezor 硬件冷钱包、Revoke.cash 授权管理、honeypot/合约扫描)、行情与图表 (TradingView、CoinGecko/CoinMarketCap)、信息与聚合 (Twitter/X、Telegram、DeFiLlama、RootData/ICO 日历、解锁日历 Token Unlocks)、自动化 (交易机器人、链上 bot/sniper、Telegram trading bot); (d) 知识正典 — 注意加密交易 canon 偏少且新: 通用交易/风控经典 (Edwin Lefèvre 'Reminiscences of a Stock Operator'、Van Tharp 'Trade Your Way to Financial Freedom' 仓位管理、Mark Douglas 'Trading in the Zone' 交易心理、Michael Mauboussin、Nassim Taleb 'Fooled by Randomness/Antifragile')、加密原生 (Bitcoin whitepaper 中本聪、'The Bitcoin Standard' Saifedean、Vitalik 博客与 Ethereum whitepaper、'DeFi and the Future of Finance'、Lyn Alden 宏观、a16z crypto 文章、Messari/Delphi/Bankless 研报)、链上分析方法 (Glassnode/CryptoQuant 教程、Nansen/Arkham/Dune 文档、Dune Analytics SQL)、交易方法论散见于 podcast/Substack/Twitter thread 而非书; (e) figures/流派 — 价值/基本面派 (Vitalik Buterin 以太坊、Hasu/Su Zhu(争议)、Arthur Hayes BitMEX 创始人/宏观+衍生品、Raoul Pal、Lyn Alden 宏观、Cobie/Jordan Fish UpOnly podcast、DeFi 研究 Bankless Ryan Adams/David Hoffman); 链上分析派 (Nansen Alex Svanevik、Arkham、Adam Cochran、Ansem(blknoiz06) 链上交易、Murad memecoin supercycle、链上侦探 ZachXBT 反诈); 合约/衍生品派 (Arthur Hayes、GCR(GiganticRebirth) 传奇合约、Pentoshi、CryptoCred 技术分析、Tyler Durden); meme/叙事派 (Ansem、Murad、Cobie、各 Solana memecoin KOL); 宏观/周期派 (Raoul Pal、Lyn Alden、PlanB stock-to-flow(争议)、Benjamin Cowen 数据/周期); 量化/系统化 (各匿名量化、Hyperliquid 生态); 中文圈 (链上分析/合约 KOL、币圈大 V、播客如 '无人之境'/'Web3 佛学院'、研究机构如 Foresight/PANews/律动 BlockBeats); 反诈/安全 (ZachXBT、SlowMist 慢雾、go+ 安全); (f) 行业话术/黑话 — 现货 spot / 合约 perps 永续 / 杠杆 leverage / 多空 long-short / 爆仓 liquidation 清算 / 资金费率 funding rate / 开多开空 / 止损 SL 止盈 TP / 仓位 position sizing / 满仓梭哈 ape in / 梭 / FOMO / FUD / 钻石手 diamond hands / 纸手 paper hands / 韭菜 / 镰刀 / 庄 / 出货 / 拉盘砸盘 / 插针 wick / 针 / 上车下车 / 埋伏 / 潜伏 / 链上 on-chain / 钱包 wallet / 地址 / 聪明钱 smart money / 巨鲸 whale / 跟单 copy-trade / 老鼠仓 / 貔貅盘 honeypot / 貔貅 / rug 跑路 rug-pull / 归零 / 土狗 (memecoin/小币) / 金狗 (暴涨百倍) / meme 币 / 叙事 narrative / 赛道 / 板块轮动 / 撸毛 撸空投 airdrop / 女巫 sybil / 交互 / 解锁 unlock / 砸盘解锁 / 代币经济学 tomomics / TVL / APY APR / 无常损失 IL / 滑点 slippage / MEV / 三明治 sandwich / gas / 抢跑 frontrun / 貔貅检测 / 授权 approve / 撤销授权 revoke / 私钥 助记词 seed phrase / 冷钱包 热钱包 / 自托管 / 减半 halving / 牛熊 / 山寨季 altseason / 比特币市占率 BTC.D / 山寨 alt / 主流币 / DeFi 暑期 / GM / WAGMI / NGMI / 归零归零 / PvP / Ponzi 庞氏; (g) 争议/批
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Builds depletion models with production decline, reserve replacement economics, and terminal value analysis for finite-life assets. Use when modeling depletion, analyzing resource longevity, or evaluating reserve life economics.
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Deconstructs unit economics with CAC, LTV, payback period, gross margin, and contribution margin analysis. Use when analyzing unit economics, validating SaaS metrics, or assessing business model efficiency.
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Use when a task needs the judgment of a Bioinformatics Scientist — designing a differential-expression or GWAS analysis with correct multiple-testing correction, calling and triaging variants from NGS data using genotype-likelihood confidence rather than raw allele counts, interpreting a BLAST/DIAMOND homology search, choosing or building a genomics pipeline (aligner, caller, normalization method) for a specific data-generating process, or judging whether a computational-biology analysis's statistical design actually supports the biological claim being made. Distinct from a bioinformatics-technician (executes and QC-gates an established pipeline someone else designed) and a data-scientist (general product/experimentation judgment, not genomics-specific statistics) — this role owns which method and statistical model a genomics question requires, and why.
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