Results for “express”

We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experi

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Expert knowledge for Azure VPN Gateway development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring S2S/P2S tunnels, BGP/NAT, IPsec/IKE crypto, VPN client auth, or cross-cloud/ExpressRoute VPNs, and other Azure VPN Gateway related development tasks. Not for Azure Virtual Network (use azure-virtual-network), Azure Virtual WAN (use azure-virtual-wan), Azure ExpressRoute (use azure-expressroute), Azure Application Gateway (use azure-application-gateway).

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Expert knowledge for Azure Virtual WAN development including troubleshooting, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring VWAN hubs, P2S/Always On VPN, BGP/IPsec routing, ExpressRoute/SD-WAN, or Private Link, and other Azure Virtual WAN related development tasks. Not for Azure Virtual Network (use azure-virtual-network), Azure VPN Gateway (use azure-vpn-gateway), Azure ExpressRoute (use azure-expressroute), Azure Traffic Manager (use azure-traffic-manager).

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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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Cell-free protein synthesis (CFPS) planning and optimization guidance. 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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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.

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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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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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Find relevant guides and runnable workflows for genomics and computational biology through an index of over 400 skills. Retrieve references or scripts for tasks such as sequence quality checks, gene expression analysis, and reporting.

• Find guidance for sequence quality checks
• Choose a gene expression analysis workflow
• Locate single-cell analysis procedures

Design reusable pose data for 2D characters, covering emotions, actions, mouth shapes, and repeated movements. Organize changes to individual body parts, pose durations, and transitions so animation sequences have clearly defined stages.

• Planning a reusable set of emotional expressions
• Designing walking and other repeated movements
• Organizing mouth shapes for a character

Perform mathematical calculations and descriptive statistics, summaries of a dataset, using information already supplied with sources. Report expressions, units, and assumptions so results can be checked, and identify missing data rather than guessing.

• Calculating from data with known sources
• Summarizing a dataset with descriptive statistics
• Checking expressions, units, and assumptions

Use SymPy to simplify expressions, solve equations, and calculate derivatives, integrals, and matrices with exact symbolic results. Specify assumptions, verify solutions, and turn mathematical expressions into numerical functions, source code, or LaTeX output.

• Solving equations and checking their solutions
• Calculating symbolic derivatives, integrals, and limits
• Finding matrix eigenvalues with exact arithmetic

Find biological pathways and functions enriched in gene lists or ranked gene data. Choose an appropriate statistical method, align gene identifiers, define comparison backgrounds, and turn results into interpretable tables and plots with multiple-testing corrections.

• Finding enriched pathways among differentially expressed genes
• Running GSEA on a complete ranked gene list
• Calculating gene-set scores for individual samples or cells

Plan protein characterization experiments with Adaptyv's cloud laboratory, estimate costs, submit sequences, track progress, and retrieve measured results. Supports binding, thermal stability, expression, fluorescence, and enzyme activity workflows through the API and Python SDK.

• Plan binding screens for candidate protein sequences
• Estimate experiment costs before submission
• Track laboratory progress and retrieve results

Review supplied writing through twelve DHDNA dimensions, a framework for describing reasoning and expression. Receive observations supported by quotations, optional scores, and comparisons between samples, with clear limits separating textual patterns from psychological traits.

• Reflect on reasoning patterns in your writing
• Compare argumentation across selected texts
• Review how a text expresses assumptions and uncertainty

Prepare bulk RNA-seq sequencing files or quantification outputs for gene-level comparisons. Check sample information and data quality, configure processing workflows, and assemble validated count tables and metadata for downstream differential expression analysis with PyDESeq2.

• Preparing gene count tables from FASTQ files
• Configuring an nf-core/rnaseq workflow
• Combining Salmon, STAR, or featureCounts outputs

Find agent skills for a specific task, compare candidates using their capabilities, sources, and installation history, and install a selected skill into Cherry after the user has expressed an intent to install it.

• Finding a skill for a specific task
• Comparing skill sources and installation history
• Installing a selected skill into Cherry