366 件 ・ 関連度順
概要と使いどころ
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.
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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.
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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), mSINGS, and MANTIS for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.
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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.
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Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).
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Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP proteomes plus colocalization triangulation, phenome-wide on-target adverse-effect scans, cross-platform Olink/SomaScan replication, and PAV (protein-altering variant) sensitivity. Use when nominating or de-risking a drug target from plasma-proteome GWAS, mimicking pharmacological inhibition via cis-pQTL instruments, separating shared-causal from LD-confounded signal under the Schmidt 2020 cis-MR framework, screening on-target adverse phenotypes pheWAS-style, or producing publication-grade STROBE-MR plus PP.H4 evidence for a target gene.
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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.
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Build one compact choice card at a genuine mathematical-modeling judgment point. Use before method screening, after a meaningful experiment, or before final claim/freeze approval so the human chooses the trade-off while AI handles mechanical consequences.
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Map contest attachments to subquestions, audit and clean raw data, and emit one reusable data profile with quality, coverage, imbalance, concentration, and method-readiness evidence for downstream risk screening.
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Systematic literature review with search, screening, and synthesis
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Continuous product discovery research operations — picking the method that fits the question, recruiting and screening participants, building interview guides, and scoring evidence into insights. Use when planning or running discovery.
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Risk-based vendor assessment framework for IT service providers, technology vendors, and third-party partners under DORA, NIS2, GDPR. Provides three-phase process (Initial Screening / Detailed Assessment / Final Evaluation), six-dimension risk scoring (Financial/Operational/Compliance/Security/Reputational/Strategic) with weighted matrices, full DORA Art. 28-30 contractual checklist, NIS2 Art. 21(2) security measures enumeration, GDPR Art. 28 documentation checks, red flags per dimension, trigger-based review criteria, and document templates. Use when: (1) Evaluating new vendors or technology providers, (2) Conducting critical ICT third-party due diligence under DORA, (3) Performing supply chain security assessment under NIS2, (4) Creating vendor onboarding documentation, (5) Establishing ongoing vendor monitoring, (6) Assessing concentration risk, or (7) Generating executive vendor risk reports.
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Turns a legal question, a set of draft questions, or source material such as a statute, jury instruction, rubric, contract checklist, or coding manual into a battery of narrow questions that TypeSafe's Jev, a fast classifier that returns probabilities rather than prose, can answer reliably across many documents. The skill breaks conclusions such as negligence, felony murder, or standing into element-level questions, writes the governing rule into each question, and delivers the questions alone, in Jev's request format or in plain English. Built for legal work that asks the same questions of many texts: coding statutes across jurisdictions, coding opinions or case files for empirical research, checking contracts against a review checklist, screening intake narratives, and grading student work against a rubric. Use when asked to write Jev questions, build a classifier for legal documents, or turn a legal test into yes-or-no questions. Running the questions requires Jev access; writing them does not.
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Elite incident response and legal compliance guidance for data breaches under GDPR Articles 33 & 34. Use when: (1) User reports a data breach or security incident — including "is this even a personal data breach?" triage, (2) User asks about breach notification obligations or deadlines, (3) User mentions "72 hours", Art. 33, Art. 34, or notification requirements, (4) Discussion involves security incidents affecting personal data, (5) User needs breach risk assessment using ENISA methodology, (6) User mentions "Data Breach" or "Incident" or "Data Leakage" or "Ransomware" or "Exfiltration", (7) User needs to determine Controller vs Processor obligations, (8) Cross-border breach scenarios requiring Lead SA determination, (9) User needs a mitigation playbook or immediate response recommendations, (10) User needs audit-ready breach documentation (.docx) or an EDPB-template-aligned breach notification / evidence file — including follow-up and withdrawal notifications, (11) Breach involves an AI system requiring AI Act Art. 73 serious incident screening.
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Use for due diligence, legal-financial risk review, investment or business transaction checklists, and preliminary screening where facts, documents, assumptions, legal uncertainty, debt/equity, assets/liabilities, contracts, tax, regulatory, compliance, technology/product, and financial-model issues must be separated clearly.
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U.S. customs and trade-law research assistant for HTS classification, CROSS ruling research, CIT/CAFC decision briefing, duty compilation (General + Special + Chapter 99 + AD/CVD + MPF/HMF), country of origin determination, FTA qualification, and end-to-end import compliance review. Triggers on product classification, tariff questions, customs rulings, trade remedy screening (Section 301/232/201), Partner Government Agency admissibility, and UFLPA forced-labor analysis. Produces attorney-reviewable draft work product with an enforced HTSUS authority hierarchy and explicit evidence ledger.
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Complete sanctions and export control analysis tool — individual designations, sectoral sanctions, dual-use goods, payment systems (SWIFT/USD), and extraterritorial regimes (EAR/ITAR/ FDPR US, ECL China). Triggers: "is X sanctioned?", "can I do business with X?", "can I sell Y to Z?", "pétrole Russie", "biens à double usage", "gel des avoirs", "sanctions internationales", "liste OFAC", "liste UE", "double usage", "embargo", "licence d'exportation", "SWIFT", "paiement en dollars", "US goods", "FDPR", "EAR", "ITAR", "BIS", "ECL chine", "no re-export clause", "sanctions sectorielles", "puis-je travailler avec X?", or any transaction involving a foreign person, product, sector, destination country, or payment in USD/EUR. Always adapt to user profile. Always run for any sanctions or export control query — even vague or exploratory ones.
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When you want to brainstorm and check available .com domains for a new project — brand naming, aftermarket pricing (HugeDomains / Afternic / Sedo / Dan), USPTO trademark screening, and social handle availability. Built on Laura Roeder's "work backwards from availability" method. Combines Vercel CLI, whois, Domainr, Namecheap, and agent-browser, each for what it reliably does. Workflow: budget → brainstorm → availability check → whois cross-check → price → aftermarket sweep (plus liveness probe and drop-watch) → bucket → negotiate → trademark + socials → buy. Triggers on "/domain," "find a domain," "check domain availability," "brainstorm a domain," "what .com is available for X," "domain hunt," "name my project," "is X.com available," "aftermarket price on X.com," "trademark check for X."
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Systematic stock screening and investment idea sourcing for A-share markets. Combines quantitative screens, thematic research, and pattern recognition to surface new long and short ideas. Adapted from the original idea-generation skill for Chinese market conventions and data sources. Triggers on "A股选股", "股票筛选", "寻找机会", "stock screen China", "A-share ideas", "find ideas for Chinese stocks", or "screen for A-share opportunities".
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The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.
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mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of g
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Use when `evidence-review` needs an operational protocol before screening and extraction.
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Use when an approved `evidence-review` protocol needs to be applied to a candidate pool.
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Screen the direction pool with a discussion-first scoring pass, writing `output/trace/IDEA_SCREENING_TABLE.md`.
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。