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Think and work like an expert Causal Inference Scientist. Use when a task calls for Causal Inference Scientist judgment. Reasons from structural causal models, potential outcomes, and identification logic through DAGs and do-calculus, doubly-robust estimators (AIPW/TMLE, IPTW, g-formula), and design-based methods (IV, RD, Callaway-Sant'Anna DiD, synthetic control) while treating colliders and M-bias, positivity/overlap failure, and unmeasured confounding (Rosenbaum bounds, E-values) as first-class failure modes.

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Think and work like an expert Astroparticle Physicist. Use when a task calls for Astroparticle Physicist judgment. Reasons from flux times cross section times acceptance, Poisson counting over structured backgrounds, and Cherenkov photoelectron budgets through SkyLLH unbinned likelihoods, Geant4/CORSIKA chains validated on through-going-muon and calibration samples, and Feldman-Cousins/CLs limits, while treating atmospheric-neutrino and downgoing-muon contamination, ER/NR leakage and the neutrino fog, and look-elsewhere trials as first-class failure modes.

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Use this skill to turn generated, captured, scanned, or modeled 3D output into production-ready standalone assets for DCC, real-time engine, web, or interchange delivery. It covers requirements, topology repair, scale and axes, UVs, PBR baking, LODs, static and skeletal readiness, rig handoff, optimization, glTF/USD/FBX delivery, validation, QA, and rights/provenance. Do not use it for provider-specific generation prompts, full scene/world building, mocap operation, or exact CAD/manufacturing work.

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Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis.

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Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

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Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.

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Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.

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Analyzes community composition using constrained ordination (CCA, RDA, db-RDA), variance partitioning (varpart), indicator species analysis (indicspecies multipatt), and distance-based environmental gradient methods with vegan. Links species composition to environmental explanatory variables. Use when testing how environmental gradients structure species communities, identifying habitat indicator taxa, or partitioning explained variation among predictors. Not for basic unconstrained ordination and PERMANOVA (see microbiome/diversity-analysis).

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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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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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End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / LHC-MR), colocalization, fine-mapping with SuSiE / FOCUS, mediation, TWAS triangulation, cis-pQTL drug-target MR, effector-gene prioritization (L2G / PoPS / cS2G), and GenomicSEM common-factor GWAS. Use when triangulating causal inference across multiple complementary methods, prioritizing tissues via stratified LDSC, nominating or de-risking drug targets, mapping a lead SNP to a candidate effector gene, modeling shared genetic architecture across correlated traits, or producing a STROBE-MR-compliant publication-grade evidence battery from GWAS summary statistics.

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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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Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when automatically annotating cell types using reference datasets.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Papers With Code MCP tools for searching and reading AI/ML papers, discovering recent and trending research, finding related work and paper lineage, browsing tasks, methods, conferences, organizations, and frameworks, and inspecting benchmark leaderboards with model-size and metric filters through the public Papers With Code catalog. Use whenever the user asks to find papers, survey literature, compare research, inspect an arXiv paper, explore AI/ML taxonomy or conferences, discover benchmarks or state-of-the-art models, or mentions Papers With Code, the PwC MCP server, or paperswithcode.co/mcp.

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Papers With Code CLI (`pwc`) for searching and reading AI/ML papers, discovering recent and trending research, finding related work and paper lineage, browsing tasks, methods, conferences, organizations, frameworks, and benchmark leaderboards, and submitting authenticated paper edits through the public Papers With Code catalog. Use whenever the user asks to find papers, survey literature, compare research, inspect an arXiv paper, explore AI/ML taxonomy or conferences, discover benchmarks or state-of-the-art models, or mentions Papers With Code, `pwc`, or `pwc-cli`.

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Guidance for using Generator.Equals — a C# source generator for auto-generating Equals, GetHashCode, operators, and Diff/Inequalities methods via attributes.

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Generate MATLAB Grader assessment items that are suitability-gated, profile-driven, feedback-aware, and validated through MATLAB MCP. Produces Script, Function, Class Definition, Class Inheritance, Object Usage, and Class Methods items with MATLAB Grader assessment setup instructions.

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Vulnerability audit and dataflow analysis built on the neug CPG engine. file_audit (default, recommended): first builds a function-level summary graph (tier1) over the entire project, then incrementally builds detailed CPGs (tier2) on demand for chosen functions; both tiers coexist in a single neug database (unified schema, cross-layer refines edges; C/Java/Python/Rust). All capabilities are exposed as CLI tool subcommands (audit/overview/build/query/methods/paths), so an agent can drive the audit step by step via shell; the audit subcommand can also run the built-in LLM loop. The same tooling also supports a dataflow analysis mode (Workflow C): no vulnerability hunting, only variable-level dataflow tracing for functions of interest, producing dataflow_analysis.json. repo_audit: multi-round LLM/Cypher audit over a full-repo CPG. Use when the user asks to audit a codebase/project for vulnerabilities, scan a project with CPG/neug, run repo_audit/file_audit, find source-to-sink taint paths, or analyze dataflow inside a function. Supports C, Java, Python, and Rust.

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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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Translates performance test results into infrastructure scaling recommendations with cost estimates. Use when someone has load test data and needs to know what infrastructure changes are required to handle target traffic. Trigger words: capacity planning, scaling plan, infrastructure sizing, how many pods, RDS sizing, handle more traffic, scale for launch.

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Design and implement Monte Carlo methods for uncertainty quantification, risk analysis, and probabilistic simulations across scientific and financial domains. Use when "monte carlo, random sampling, uncertainty quantification, risk analysis, stochastic simulation, MCMC, variance reduction, probabilistic, " mentioned.

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