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Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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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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Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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Automate Attio CRM operations -- search records, query contacts and companies with advanced filters, manage notes, list attributes, and navigate your relationship data -- using natural language through the Composio MCP integration.

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Expert-level medicinal chemistry knowledge. Use when working with drug design, structure-activity relationships, ADMET properties, pharmacophores, lead optimization, target identification, drug metabolism, or pharmaceutical development. Also use when the user mentions 'SAR', 'drug design', 'pharmacophore', 'ADMET', 'lead compound', 'hit to lead', 'drug metabolism', 'bioavailability', 'selectivity', 'binding affinity', 'scaffold hopping', or 'bioisostere'.

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Use for any question about a codebase, its architecture, file relationships, or project content — especially when graphify-out/ exists, where the question should be treated as a graphify query first. Turns any input (code, docs, papers, images, videos) into a persistent knowledge graph with god nodes, community detection, and query/path/explain tools.

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Design relational database schemas (and choose when to go NoSQL) that stay maintainable and fast. Use this skill whenever the user mentions tables, DDL, entities and relationships, normalization (1NF/2NF/3NF), primary and foreign keys, UUID vs bigint IDs, indexes (B-tree, composite, covering, partial), EXPLAIN, constraints (CHECK, UNIQUE, exclusion), transactions and isolation levels, migrations (Alembic, Prisma, Flyway, expand-contract, backfilling), or SQL vs NoSQL (MongoDB, DynamoDB, Cassandra, graph databases). Also trigger for "design the database", "model this domain", "which database should I use", or writing ORM models and migration files for PostgreSQL, MySQL, SQLite, or SQL Server.

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Manages government affairs, public policy communications, and collective action aligned with B Corp GACA standards. Creates policy position papers, advocacy communications, regulatory response documents, and transparent lobbying reports. Use when user asks about government relations, public policy, advocacy, lobbying, regulatory affairs, collective action, or political engagement transparency.

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Creates stakeholder communications including investor updates, board reports, annual impact reports, and partner communications aligned with B Corp PSG standards. Use when user asks about investor relations, board communications, stakeholder reporting, impact reports, annual reports, or partner/supplier communications.

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Use when writing Eloquent models, relationships, scopes, or queries via Model:: — 'fetch users with their orders'. NOT for PHPStan output, non-Eloquent services, or raw SQL questions.

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Use when designing churn defence — health-score signals, churn-cause split (involuntary / value / relationship / fit), early-warning loop. Triggers on 'why are accounts leaving'.

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[Code Intelligence] Use when you need to query code relationships and connections using the structural knowledge graph.

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Guidelines and strategies for constructing meaningful test suites, property-based tests, metamorphic relations, and fuzzing harnesses. Trigger when: - Designing verification bounds, writing tests, creating test invariants, or implementing validation gates. - Prompt contains: testing, test design, property-based testing, PBT, metamorphic testing, fuzzing, integration tests, E2E.

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Render a crouton collection schema (the field-definition JSON) into a human-readable field table + relationships sketch (HTML + PNG + a terse Markdown table), so a human can sign off on the DATA MODEL before any code is generated. Use when an agent drafts or changes a collection schema (before `crouton config` / `generate_collection`), or when asked to "review a schema", "show the data model", "check these fields".

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融合《如何避免孤独终老》(Logan Ury) 关系决策框架与《寻找你的维他命人》(Marian Rojas Estapé) 关系生物学框架。适用于用户想改善亲密关系或社交质量、诊断"为什么总是遇到同类型的人"或"为什么关系总是无法深入"、设计社交策略或约会决策框架、处理关系中的冲突与修复、以及评估一段关系是否值得继续投入时使用。

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Design and generate Convex database schemas with proper validation, indexes, and relationships. Use when creating schema.ts or modifying table definitions.

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Explain an existing Convex app — data model + relationships, public vs internal functions, auth/ownership model, components, a request→data flow — read from the schema and function surface. Read-only.

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Explain an existing Convex app — data model + relationships, public vs internal functions, auth/ownership model, components, a request→data flow — read from the schema and function surface. Read-only.

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。