785 件 ・ 関連度順
概要と使いどころ
Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).
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Communicate an integrated insight in a way that is accessible, actionable, and preserves the multi-domain nature of the understanding. Integrated insights are multi-dimensional — linearizing them risks losing the relationships that make them valuable. This skill provides a structured procedure for choosing the right form, expressing the gestalt with honest attribution, and inviting productive challenge. Use after integrate-gestalt has formed a cross-domain understanding that needs to be communicated to an audience — domain specialists, generalists, or decision-makers.
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Modern PHP idioms for any PHP project (PHP 8.1+): readonly properties, enums, match expressions, constructor property promotion, typed properties, named arguments, nullsafe operator, first-class callable syntax, strict_types, PSR-12 style, and null discipline. Apply when the project is a PHP 8.1+ project. Stack-agnostic — referenced by every PHP plugin in the marketplace. Use this skill to: - Write strongly-typed, immutable-by-default value objects with readonly properties and enums. - Replace switch ladders and magic constants with match expressions and backed enums. - Cut constructor boilerplate with property promotion and express optionality with typed nullable returns. - Keep code PSR-12 compliant with declare(strict_types=1) in every file. Do NOT use this skill for: - Framework-specific idioms (Eloquent, Doctrine, Symfony services, Laravel facades — those live in framework plugin skills). - Composer / autoloading / dependency management — see php-foundation:composer-tooling. - Testing patterns — see php-foundation:php-testing.
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Expression Language injection playbook. Use when Java EL, SpEL, OGNL, or MVEL expressions may evaluate attacker-controlled input in Spring, Struts2, Confluence, or similar frameworks.
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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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Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).
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End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment. Orchestrates temporal DE (limma splines or DESeq2 LRT), Mfuzz/tslearn soft clustering of expression-profile shapes, GAM trajectory fitting, per-cluster GO enrichment against a temporal-gene background, and an OPTIONAL circadian rhythm-detection branch (MetaCycle/CosinorPy) that runs only when the design covers >=2 full cycles with >=6-8 evenly spaced samples per cycle. Use when analyzing a bulk time-series expression experiment from any omics platform and deciding limma-splines vs DESeq2-LRT for temporal DE, soft vs hard clustering, whether the sampling design even licenses rhythm detection, and which background to use for enrichment. Not for single-cell pseudotime (see temporal-genomics/trajectory-modeling for the bulk-vs-pseudotime boundary) or unknown-period discovery (see temporal-genomics/periodicity-detection).
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Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA, rWikiPathways), and visualize. Use when a DESeq2/edgeR/limma result must become enriched GO terms, KEGG/Reactome/WikiPathways pathways, or a GSEA leading edge; when the input is a full ranking for all genes (GSEA, named decreasing vector) or only a pre-selected list (ORA plus a defensible background universe); or when assembling DE-to-pathway end to end. The DE list and ranking statistic come from differential-expression/de-results; per-method nuance lives in the pathway-analysis skills.
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。
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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Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse expression inputs, and network stability checks.
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Comprehensive backend development guide for Node.js/Express/TypeScript microservices. Use when creating routes, controllers, services, repositories, middleware, or working with Express APIs, Prisma database access, Sentry error tracking, Zod validation, unifiedConfig, dependency injection, or async patterns. Covers layered architecture (routes → controllers → services → repositories), BaseController pattern, error handling, performance monitoring, testing strategies, and migration from legacy patterns.
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Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
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。
Comprehensive backend development guide for Node.js/Express/TypeScript microservices. Use when creating routes, controllers, services, repositories, middleware, or working with Express APIs, Prisma database access, Sentry error tracking, Zod validation, unifiedConfig, dependency injection, or async patterns. Covers layered architecture (routes → controllers → services → repositories), BaseController pattern, error handling, performance monitoring, testing strategies, and migration from legacy patterns.
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。
Run or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.
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Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries
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Add strategic color to features that are too monochromatic or lack visual interest, making interfaces more engaging and expressive. Use when the user mentions the design looking gray, dull, lacking warmth, needing more color, or wanting a more vibrant or expressive palette.
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Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use the cell2location, DestVI, or Tangram methods instead.
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Hunt server-side template injection (SSTI) across Jinja2 (Flask/Django), Twig (Symfony), Freemarker (Java), ERB (Rails), Spring, Velocity, Mako, Thymeleaf, Smarty. Detection probes use double-curly and dollar-curly math expressions evaluated server-side. Once an engine is fingerprinted, escalate to RCE via the engine-specific class-walker, callback-registrar, or Execute-utility patterns documented in disclosed reports. Detection patterns: error messages reveal engine, blank or numeric eval reveals expression mode. Targets: email templates, PDF/report generators, CMS preview features, error pages with user input. Use when hunting RCE via template rendering, when content shows engine fingerprints, when finding endpoints that compose strings with user input before render.
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Hunt Node.js specific vulnerabilities — Prototype Pollution → RCE chains (lodash/merge/assign), Express trust proxy misconfiguration, child_process/eval injection, template engine SSTI (EJS/Pug/Handlebars), path traversal in file servers, require() injection, environment variable exfil via /proc/self/environ. Use when target runs Node.js/Express/Fastify/NestJS/Koa.
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Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
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。
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
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。
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
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Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
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Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.
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。