「cis」の検索結果

Orchestrator for the pre-decision business-idea lifecycle — generate ideas, model them, evaluate them, validate them with customers, and only then hand off to product-soul / brainstorming. Routes through `idea-generation`, `business-modeling`, `idea-evaluation`, and `customer-discovery`. Load when the user asks to explore business ideas, find a startup idea, evaluate a venture, validate an idea, says "what business should I start", "should I build this", "is this a good business", "I have a startup idea", "evaluate this venture", "model this business", "validate this idea", "Mom Test this", "Lean Canvas this", "Business Model Canvas", "Value Proposition Canvas", "go/no-go on this idea". Pre-decision suite — once one idea is committed, hands off to `product-soul`. Does NOT design features (use `brainstorming`) or audit built products (use `reality-check`).

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Write a rigorous, decision-grade experiment spec — falsifiable hypothesis, primary metric, guardrails, randomisation unit, exposure definition, method (A/B, holdout, switchback, quasi-experiment, MAB), MDE/duration plan, peek policy, validity threats, and pre-committed decision rule. Platform-agnostic. Load when the user has a candidate experiment and needs to spec it before launch, or says "spec this experiment", "write the test plan", "design this A/B test", "what's the hypothesis", "how big a sample do we need", "how long should we run this", "define the metrics for this test", or when the experimentation orchestrator routes here.

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Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.

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Architectural decision-making framework. Requirements analysis, trade-off evaluation, ADR documentation. Use when making architecture decisions or analyzing system design.

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Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Decision-theoretic framework for agents embedded within the environments they model and act upon

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Audit whether a "current product focus receipt" (Decision/Now/Why-now/Evidence/Not-now/Cut-suspend/First-visible-proof/ Acceptance-gate/Kill-revisit-trigger/Owner/Review-date) and the work order it gates state a real, testable decision and a real agent launch — not planning-placeholder prose that sounds like an assignment but can't be proven. Use when deciding whether to launch an agent chain against a milestone or a stated "focus," when a work order lacks explicit input/output/owner/proof-gate, or when an acceptance gate would only prove a cached UI state instead of daemon truth. NOT for distinguishing roadmap items from energy-driven sidequests (legible-roadmap-with-sidequests), reviewing a PRD/prototype for product-completeness gaps like cold start or pricing (product-reality-reviewer), or accepting already-finished work against a personal acceptance bar (port-daddy-user-surrogate-pm-review).

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The interview primitive for putting open decisions to an owner. Use on 'grill me', 'stress-test this', or 'what do you need from me before you build this', and whenever a plan, scope, spec, vision, or question ledger needs owner rulings. NOT for steps only a human can perform (use a guided session).

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The gate and path for any question an agent wants Arman to decide. Use when about to ask him anything, ending a turn on a question for him, writing 'needs Arman's decision', marking work blocked on him, or on /ask-arman. NOT for a step only he can perform (use a guided session).

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Conduct market research, competitive analysis, investor due diligence, and industry intelligence with source attribution and decision-oriented summaries. Use when the user wants market sizing, competitor comparisons, fund research, technology scans, or research that informs business decisions.

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Codified expertise for returns authorization, receipt and inspection, disposition decisions, refund processing, fraud detection, and warranty claims management. Informed by returns operations managers with 15+ years experience. Includes grading frameworks, disposition economics, fraud pattern recognition, and vendor recovery processes. Use when handling product returns, reverse logistics, refund decisions, return fraud detection, or warranty claims.

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。

Architectural decision-making framework. Requirements analysis, trade-off evaluation, ADR documentation. Use when making architecture decisions or analyzing system 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。

Strategic advisor for Evvo Labs business decisions. Use when Vince asks for strategic advice, business opinions, market entry decisions, pricing strategy, product prioritization, resource allocation, partnership evaluation, competitive positioning, or any question about what Evvo should do next. Applies 5 frameworks: VRIO (competitive advantage), Value Stick (pricing/margin), Blue Ocean (market positioning), McKinsey Horizons (resource allocation), Strategy Diamond (initiative planning). Always read references/evvo-strategy.md before advising.

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Decision-making advisor using Tree of Thoughts for exploring options, analyzing trade-offs, and providing data-driven recommendations.

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Decision validation and thinking frameworks for startup founders. Use when you need to pressure-test a decision, validate your next steps, think through strategic options, or sanity-check your approach. Triggers on phrases like "should I", "help me think through", "is this the right move", "validate my thinking", "what am I missing". Covers fundraising, customer development, runway management, prioritization, and crypto/web3 founder challenges.

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Multi-Agent group chat collaboration system inspired by DingTalk/Lark. Enables AI agents to chat in groups, @mention each other, assign tasks, make decisions via voting, and collaborate. Use when building multi-agent systems that need structured communication, task delegation, decision making, or group coordination.

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Consult a virtual board of 4 strategic advisors (Donald Miller, Seth Godin, Alex Hormozi, Daniel Priestley) on any major business decision. Two rounds of argument + rebuttal, then a decision brief, interactive dashboard, and clear recommendation.

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Grilling session that challenges your plan against the existing domain model, sharpens terminology, and updates documentation (GLOSSARY.md, ADRs) inline as decisions crystallise. Use when user wants to stress-test a plan against their project's language and documented decisions.

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。