Results for “expression”

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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Visual expression system for AI personas with emotion-based face switching. Use at session start to display the expression UI, and switch expressions whenever the emotional state changes during conversation.

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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.

The English summary is being prepared. Showing the original description.

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.

The English summary is being prepared. Showing the original description.

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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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.

• Integrating single-cell RNA data across experimental batches
• Assigning cell labels using partial annotations or a reference
• Analyzing RNA with protein or ATAC measurements

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.

• Choosing a protein expression and purification protocol
• Preparing inputs for mRNA or circRNA synthesis
• Reviewing stability assays and measurement method setup

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.

• Looking up gene details and sequences
• Exploring protein structures and residue annotations
• Comparing tissue expression and disease associations

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.

• Investigate why a cloud flow failed
• Find null values or incorrect field paths in expressions
• Inspect HTTP error response details

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.

• Reviewing GitHub Actions workflow security
• Checking action version pinning
• Finding unsafe event expressions in scripts

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.

• Vary repeated words in a piece of writing
• Choose wording for formal or conversational contexts
• Compare subtle differences between similar words

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.

• Create patterns for extracting text
• Explain unfamiliar regular expressions
• Fix unwanted matches and missed matches

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.

• Looking up healthy wild-type expression metadata
• Searching with relationships between biological terms
• Checking whether matching data exists

Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation. Reach for this skill when designs from vanilla ProteinMPNN are aggregating or going to inclusion bodies, when redesigning a membrane-adjacent fold for soluble expression, or when an E. coli expression screen is the next step.

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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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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 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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Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. NOT for:single-cell RNA-seq, methylation analysis, non-expression data.

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Use when implementing a new Spark expression in DataFusion Comet. Walks through cloning latest Spark master to study the canonical implementation, checking the upstream datafusion-spark crate before writing native code, building the Comet serde and Rust wire-up from the contributor guide, then running audit-comet-expression to drive a test-coverage iteration loop.

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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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Author, validate, and test Power Query M expressions in semantic model partitions. Automatically invoke when the user mentions "Power Query", "M code", "M expression", "partition expression", "query folding", or asks to "write Power Query", "fix Power Query", "test a partition", "preview partition data", "debug Power Query step", "optimize Power Query".

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