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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of 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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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Use when users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

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Evaluate design from a UX perspective, assessing visual hierarchy, information architecture, emotional resonance, cognitive load, and overall quality with quantitative scoring, persona-based testing, and actionable feedback. Use when the user asks to review, critique, evaluate, or give feedback on a design or component.

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Extract product data, prices, reviews, and seller information from any e-commerce platform using Apify's E-commerce Scraping Tool.

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Discover and track emerging trends across Google Trends, Instagram, Facebook, YouTube, and TikTok to inform content strategy.

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Fetch any X/Twitter post as clean LLM-friendly JSON. Converts x.com, twitter.com, or adhx.com links into structured data with full article content, author info, and engagement metrics. No scraping or browser required.

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SwiftUI UI component catalog. Use when implementing NavigationStack, Swift Charts, PhotosPicker, TipKit, ScrollView enhancements, animations, layouts, WebView, Liquid Glass and other UI components. Organized by feature category with OS version compatibility info. Reference for discovering available components and implementation patterns.

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Extract EPA/NADP tDEP atmospheric deposition and NADP precipitation chemistry rasters for an AmeriFlux or EcoSIM site. Use when deriving atmospheric chemistry inputs such as NH4, NO3, SO4, Ca, or precipitation pH for EcoSIM forcing workflows.

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Prepare, validate, and edit EcoSIM plant management inputs using pft_mgmt_in NetCDF, editable Excel workbooks, and optional PlantMgmtWriter.py JSON files. Use when creating or checking natural PFT management data, converting pft-mngt NetCDF to an Excel sheet for editing, converting edited Excel back to JSON or NetCDF, validating pft_type/pft_pltinfo/pft_mgmt entries, or preparing PlantMgmtWriter.py inputs for EcoSIM.

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Extract study sites, observational variables, coordinates, climate-forcing sources, and cited data sources from ecosystem-modeling papers, PDFs, supplements, or article text, then plan or create EcoSIM simulation workflows and run folders for those sites. Use when Codex is asked to read a paper for EcoSIM feasibility, including requests phrased as "read paper for ecosim feasibility"; read a paper for sites/data availability; reproduce a published site simulation in EcoSIM; compare EcoSIM outputs to paper observations; or convert paper-derived AmeriFlux, FLUXNET, US NLDAS-domain, non-US ERA5, crop, peatland, forest, grassland, wetland, or unmanaged field-site information into EcoSIM inputs and runnable cases.

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Extract AmeriFlux site metadata and map it to EcoSIM JSON variables. Use when a task needs site latitude, longitude, elevation, mean annual temperature, Koppen climate code, or vegetation type for an AmeriFlux site ID or flux-site name.

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Hand-drawn, sketch-like style with doodles, handwritten fonts, and imperfect lines for a playful, informal feel.

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Use when the user wants a code review of an explicit range or set of files — correctness, security, performance, conventions, tests — with stable findings (CR-nnn, BLOCKER..INFO) and rule citations — 'revisar os últimos commits', 'code review da feature X', 'review base..HEAD'. Plans a REPORT-mode review (no code changes, no commit). Do NOT use to fix code (feat-feature / feat-quick), to write tests (feat-test) or for UI/UX design critique.

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Add a standard AdwAboutDialog wired to app metadata, plus the AppStream metainfo file it should share data with. Use when adding an About entry, release notes, credits, or preparing app metadata.

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When the user wants to conduct, analyze, or synthesize customer research. Use when the user mentions "customer research," "ICP research," "talk to customers," "analyze transcripts," "customer interviews," "survey analysis," "support ticket analysis," "voice of customer," "VOC," "build personas," "customer personas," "jobs to be done," "JTBD," "what do customers say," "what are customers struggling with," "Reddit mining," "G2 reviews," "review mining," "digital watering holes," "community research," "forum research," "competitor reviews," "customer sentiment," or "find out why customers churn/convert/buy." Use for both analyzing existing research assets AND gathering new research from online sources. For writing copy informed by research, see copywriting. For acting on research to improve pages, see page-cro.

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