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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting treatment effects in confirmatory trials, comparing effect sizes across studies, or constructing forest plots.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 16a.

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Calculate the Maryland Aggregate Pathology Index (MAPI) on a deceased donor procurement kidney biopsy to predict graft survival and decide single vs dual vs discard allocation. Trigger when a clinician asks "what's the MAPI score", "interpret donor kidney biopsy", "should I use this marginal kidney", "MAPI cutoff for transplant", "procurement biopsy scoring", or has histology results from a deceased donor kidney and needs an objective grading.

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Act as a senior Amazon account growth operator that combines Amazon performance-drop analytics, Amazon growth-opportunity analytics, Amazon Ads data, retail readiness, BSR/rank signals, margin, inventory, and campaign/search-term evidence into a prioritized profitable growth action plan. Use when Codex needs to decide what to protect, fix, scale, reduce, pause, harvest, launch, or monitor for an Amazon brand, agency, marketplace, ASIN set, or account; when building daily, weekly, or monthly Amazon account operating plans; when reallocating ad budget; when deciding which ASINs are safe or risky to push; or when turning performance-drop and growth-opportunity findings into approval-gated actions with success/failure criteria.

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Use when modeling CAC, LTV, payback, contribution margin, or burn-multiple per customer — SaaS, marketplace, or transactional. Triggers on 'are we unit-economic', 'what is our LTV/CAC'.

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Guides continuous improvement and change management for SMEs adopting AI. Applies Marginal Gains philosophy, Kaizen principles, and structured sprint methodologies to organizational transformation. Use when user asks about change management, continuous improvement, AI adoption strategy, team resistance, transformation roadmaps, or improvement sprints.

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Validate and implement Sinclair ZX81 video emulation in the EMULATORS repository for /mZX811, /mZX812, and /mZX813, including ULA character generation, Z80 display-file execution, M1/refresh/HALT/INT behavior, scanline timing, HSYNC/VSYNC, NMI generator and WAIT synchronization, SLOW and FAST modes, PAL/NTSC margins, collapsed display files, inverse video, high-resolution techniques, ROM-version interactions, and ULA revision boundaries. Use when Codex reviews or edits namespace ZX81 ULA, ULARegisters, MemoryVideoCode, Memory, PortManager, Screen, CPU interrupt timing, raster, ROM-specific video flow, or ZX81 video tests.

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Generate QR code images from text, URLs, or contact information using Python's qrcode library. Supports customization (size, margin, color, error correction) and batch generation.

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Reviews a proposal, business case, deck or plan in character as a Chief Marketing Officer archetype and returns a DRAFT review in the chat with a verdict, findings cited to specific passages, marketing risks, what would change the verdict and five interrogation questions. Use when the user asks to "run a CMO review", "pressure-test the positioning", "what would a CMO say about this", "challenge the launch plan" or "check the messaging and audience". Do not use for price economics, margins or payback, use cfo-reviewer instead; for sales pipeline mechanics, use cro-reviewer. Drafts for human review; never approves, authorises or signs off.

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Knowledge base from the NASA Schedule Management Handbook (2024 edition, Revision 2). Use for program/project schedule management of aerospace and large engineering efforts: the five sub-functions (Planning, Development, Assessment & Analysis, Maintenance & Control, Documentation & Communication); the Integrated Master Schedule (IMS) and the WBS/OBS/CBS breakdown structures; the Schedule Management Plan (SMP) and Basis of Estimate (BoE); Critical Path Method, logic, durations, float and margin; tiered schedule assessment (Requirements/Health/Basis checks, the Shock Test) and the Dimensions of Schedule Reliability; Schedule Risk Analysis (SRA), Integrated Cost-Schedule Risk Analysis (ICSRA), Monte Carlo, correlation, merge bias, and the Joint Confidence Level (JCL); baselining, replan vs. rebaseline, EVM schedule metrics (SPI, BEI, CEI, HMI, Earned Schedule, CPLI), and status/progress/forecast reporting. This is NASA's scheduling doctrine grounded in NPR 7120.5 and the GAO Schedule Assessment Guide. Thin on the underlying mechanics of CPM, statistics, and EVM (it points to companion handbooks); aerospace/space-flight-centric; anchored to the 2024 second edition.

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Plan and review paid-media budgets, bidding, pacing, marginal return, forecasts, CPA, ROAS, MER, LTV:CAC, constraints, and allocation across supported platforms. Use for ad budget allocation, media budget, bidding strategy, scaling, spend pacing, budget forecast, ROAS target, or investment tradeoffs.

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Marketing analytics and data-driven optimization for B2B SaaS campaigns. Use this skill when analyzing marketing performance, optimizing conversion rates, running A/B tests, conducting customer research, creating marketing dashboards, building attribution models, analyzing funnel metrics, or storytelling with data. Also triggers on: marketing ops, performance analytics, CRO, A/B testing, data storytelling, customer insights, tracking plan, event taxonomy, UTM taxonomy, GA4 audit, consent mode, instrumentation contract, sample size calculation, minimum detectable effect, test duration, not enough traffic to A/B test, statistical significance, Bayesian vs frequentist, sample ratio mismatch, experiment feasibility, martech stack, marketing tech stack audit, tool consolidation, build vs buy, vendor evaluation, shadow IT tools, ESP/CRM/platform migration, switching cost, cutover plan, suppression list migration, data portability, customer interviews, survey design, sampling frame, non-response bias, how many people should I interview, thematic saturation, voice of customer, jobs-to-be-done, buyer persona research, is this finding real, data enrichment, which enrichment provider should we buy, waterfall enrichment, contact data quality, match rate, our list data is bad, email verification, catch-all domain, accept-all, bounce rate from bad data, B2B data decay, how often should we re-verify contacts, ZoomInfo vs Apollo vs Clearbit evaluation, cost per usable record, where did this list come from, GDPR Article 14 notice, purchased list compliance, suppression screening, TAM list building, demand planning, marketing plan, how many leads do we need, what pipeline target should marketing carry, funnel model, top-down vs bottom-up plan, plan of record, annual marketing planning, quarterly planning, pipeline coverage we have to create, sales cycle lag, our leads cannot close this quarter, carry-in pipeline, scenario planning, conservative moderate aggressive forecast, stretch target, reforecast, re-forecast triggers, assumption register, capacity ceiling, addressable audience ceiling, marginal cost per lead, blended CPL is wrong, we missed plan and nobody knows why.

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Calculate and model paid-media CPA, CPL, CPC, CPM, ROAS, MER, break-even targets, contribution margin, LTV:CAC, impression-share opportunity, budgets, forecasts, and experiment economics. Use for PPC math, ad calculator, break-even analysis, ROAS calculator, CPA calculator, budget forecast, LTV CAC, or MER.

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Applies a modern CSS reset covering box-sizing, margin removal, text rendering, media defaults, and root stacking context. Use when starting a new web project, creating a global stylesheet, or when the codebase lacks sensible CSS defaults.

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Assess a company's economic moat, EBITA margin trajectory, and organic growth trajectory from analyst reports, earnings transcripts, or long-form articles. Produces structured qualitative outlook that feeds into the Financial Modeling skill's assumption generation.

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Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting treatment effects in confirmatory trials, comparing effect sizes across studies, or constructing forest plots.

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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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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 7.

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End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting. Covers data preparation, FDA 2023 marginal vs conditional logistic regression, categorical tests with Boschloo, modern HTE/subgroup methods, missing-data sensitivity (MMRM, reference-based MI, Permutt tipping point), graphical multiplicity (Bretz-Maurer), survival analysis (Cox/RMST/competing risks) when applicable, and Table 1. Use when performing a complete analysis of clinical trial data.

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Open and manage short positions on HoneyComb job tickers. Profit when a ticker's price drops. Covers opening shorts with collateral, closing (full/partial), margin withdrawal, liquidation risk, and position health monitoring. Use when betting against a job position or hedging long exposure.

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Use when job costing a construction or contracting job: committed against actual cost, labour, plant, subcontract and materials allocation, margin by contract, variance to budget, and the cost-to-date and cost-to-complete figures the WIP calculation consumes.

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Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca (Illumina, repeat-aware), Pilon (legacy short-read), NextPolish/NextPolish2, Hapo-G (haplotype-aware), ntEdit, and DeepPolisher/PEPPER-Margin-DeepVariant for human. Covers the do-not-polish-HiFi rule, the medaka basecaller-model footgun, held-out Merqury QV as the only honest stop signal, and the haplotype-collapse trap. Use when correcting homopolymer indels or residual SNPs in a long-read assembly, deciding if a HiFi assembly needs polishing, or choosing an ONT vs hybrid vs short-read polishing chain.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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