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Validate n8n expression syntax and fix common errors. Use when writing n8n expressions, using {{}} syntax, accessing $json/$node variables, troubleshooting expression errors, or working with webhook data in workflows.
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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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Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.
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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.
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Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.
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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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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.
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Fit probabilistic models to single-cell measurements for integration across experiments, cell annotation, combined RNA and protein or ATAC analysis, and gene expression comparisons. The skill covers input requirements, training checks, reference mapping, and interpretation of model uncertainty.
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Look up genes, sequences, protein structures, expression patterns, and disease associations across more than 20 bioinformatics resources using command-line tools or Python. Useful for interactive exploration, with results that can be saved for further analysis.
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Prepare experiments for Ginkgo Cloud Lab by choosing a protocol, organizing required inputs, checking configured pricing, and navigating browser ordering. Covers protein expression, RNA synthesis, stability assays, and setup of measurement methods.
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Investigate failed Power Automate cloud flows through FlowStudio MCP. Inspect each action’s inputs and outputs, trace incorrect data upstream, fix expression or data issues, and replay a previous run to check the repair.
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Audit GitHub Actions workflows and CI/CD configurations for supply chain risks. Use Python and YAML parsing to identify unpinned actions, unsafe event expressions, excessive permissions, dependency confusion, and potential exposure of secrets in build pipelines.
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Find alternative words and phrases that fit a sentence, audience, and tone. Suggestions distinguish close synonyms from related expressions, explain differences in meaning or formality, and include brief usage examples when helpful.
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Design and build backend services with API scaffolding, database migrations, authentication reviews, and load testing. Generate route handlers from OpenAPI specifications, identify PostgreSQL optimization opportunities, and compare architecture choices against traffic, data sensitivity, and reliability requirements.
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Helps create, explain, debug, and optimize regular expressions for finding, extracting, or replacing text. Accounts for differences between programming languages and checks matching and nonmatching examples to identify overly broad patterns and potential performance problems.
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Add a dashboard or admin panel across the server and interface. This skill follows existing project patterns to build API routes, service logic, components, registration, and styles, then connects request handlers so the new endpoint is reachable.
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Query Bgee for healthy wild-type gene expression metadata and receive concise summaries. The skill supports lookups that account for relationships between biological terms, keeps requests small, and saves raw results only when requested.
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Write and review GitHub Actions workflows for syntax and structural correctness. Check quoting around expressions and special characters, then validate with actionlint, a workflow checker, to catch errors that ordinary YAML parsing can miss.
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Use SymPy in Python to solve equations, simplify formulas, calculate derivatives and integrals, and work with matrices. Keep exact results such as fractions and square roots, then turn expressions into executable code or LaTeX.
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Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when analyzing time-series or longitudinal expression data.
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Amazon Aurora PostgreSQL — creates, modifies, and advises on Aurora PostgreSQL clusters specifically (PostgreSQL-compatible engine, Aurora serverless, express configuration, pgvector, Babelfish). Trigger for Aurora PostgreSQL cluster operations, express-configuration quick-start, ACU sizing, I/O-Optimized storage, commitment pricing, or PostgreSQL upgrade planning. For Aurora MySQL, use amazon-aurora-mysql instead. Contains safety guardrails, express-first routing, and response templates that override defaults.
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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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Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG analysis, volcano plot, clustered heatmap, limma-based two-group comparison, and case-vs-control screening. NOT for single-cell RNA-seq, multi-group contrasts, count-model workflows such as DESeq2/edgeR, or non-expression omics data.
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Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.
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