Results for “annotation”

Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware differential and enrichment analysis with lipidr, guarding against in-source-fragment phantoms, sn-position over-claims, and invalid cross-class quantification. Use when naming or canonicalizing lipid species (shorthand separators, Goslin), deciding shotgun vs RP vs HILIC LC-MS, picking internal standards (SPLASH/EquiSPLASH), interpreting MS-DIAL/LipidSearch output, or comparing lipid classes. For general feature detection see metabolomics/xcms-preprocessing and metabolomics/msdial-preprocessing; for non-lipid annotation confidence see metabolomics/metabolite-annotation; for normalization/QC see metabolomics/normalization-qc; for multivariate stats see metabolomics/statistical-analysis.

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Turns untargeted LC-MS/MS features (m/z, RT, MS/MS) into confidence-stratified metabolite annotations using spectral-library matching (matchms), in-silico tools (SIRIUS/CSI:FingerID, MetFrag) and molecular networking, and assigns a defensible MSI/Schymanski confidence level to each. Use when naming detected features, scoring MS/MS against a reference library, running SIRIUS, or deciding what confidence level an evidence set actually supports. For upstream feature extraction see metabolomics/xcms-preprocessing and metabolomics/msdial-preprocessing; for downstream enrichment that must respect these levels see metabolomics/pathway-mapping; for lipid-specific structural annotation see metabolomics/lipidomics.

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Design data annotation workflows for AI. TRIGGERS - Use when user needs help with ai-annotation-workflow related tasks.

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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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Use SAM to separate objects from images by marking points or drawing boxes, without training a model for each task. Covers automatic region generation, refining selections, preparing annotation data, and exporting models for deployment.

• Extract an object with a transparent background
• Build an interactive image annotation tool
• Generate region masks for vision model training

Create a hand-drawn HTML wireframe for exploring screen layouts before detailed design. Graph paper, sticky notes, sketch tabs, and rough chart placeholders present an early concept with annotations for discussion and review.

• Sketching an initial portal or dashboard layout
• Presenting layout options with labeled sketch tabs
• Adding review notes to an early screen concept

Create a Swiss-inspired presentation page as a single HTML file, using bold typography and geometric cards. The template includes slide navigation, light and dark themes, accent color cycling, and optional annotation overlays without external runtime dependencies.

• Build a presentation-style landing page
• Create a Swiss-inspired HTML slide deck
• Present a launch with interactive navigation

Apply consistent deprecation notices to public Remotion APIs that remain available. Use TypeScript annotations and documentation formatting to mark APIs as no longer recommended, identify replacements, and review whether both representations follow the conventions.

• Marking an existing public API as deprecated
• Adding guidance on a replacement API
• Reviewing deprecation annotations and documentation

Process mass spectrometry data using scripts for format conversion, signal cleanup, peak detection, and quantification across samples. Prepare protein and metabolite analyses with identification filtering, candidate annotations, data tables, and plots.

• Inspect, convert, and preprocess mass spectrometry files
• Build quantitative tables across multiple samples
• Find metabolite candidates from accurate mass

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

Search the 1000 Genomes Project’s 3,202 participants for genetic variants and their carriers. Filter by frequency or annotations, inspect variants in selected individuals, and check relatedness between two participants.

• Find participants carrying variants that match specified criteria
• Inspect genetic variants carried by selected participants
• Identify participants with two reference copies at a position

Create shareable links that open specific Arize resources, including traces, datasets, and evaluators. Use IDs from logs or exported data, with suitable time ranges, to direct teammates to the relevant view.

• Share a trace with teammates
• Open an Arize view from IDs in logs
• Link directly to a dataset or evaluator

Use SAM to identify object regions in images from points, boxes, or existing masks. The skill provides implementation examples for transparent cutouts, automatic mask generation, annotation tools, and model selection based on available resources.

• Extracting objects with transparent backgrounds
• Building annotation tools with point or box selection
• Generating object masks automatically

Turn a Markdown code review into a single HTML file with code changes beside severity-labeled comments. Readers can jump to findings, inspect line numbers, and identify the named human reviewer.

• Turning a lengthy Markdown code review into HTML
• Reading code changes beside review comments
• Jumping directly to findings by severity

Turn long Markdown files into a single HTML file for reading, reviewing code, or presenting slides. Routes each input to a specialized converter and applies shared design settings, with navigation and interaction suited to the document type.

• Converting long specifications or reports into navigable HTML
• Presenting code reviews with diffs and severity annotations
• Turning Markdown into slides with keyboard navigation

Audit multilingual and regional websites for hreflang errors, the annotations that connect language versions. Generate corrected tags or sitemaps, and check for missing translations, inconsistent local formats, and content that needs cultural adaptation.

• Check language and region annotations before a multilingual launch
• Generate a sitemap connecting pages across regional domains
• Find missing or outdated translations across language versions

Build Lightweight Charts™ plugins that add custom chart types, annotations, or overlays. The skill guides plugin selection, project setup, implementation with official helpers, testing of drawing and interactions, and preparation for publishing.

• Add a custom chart type
• Draw annotations or watermarks on a chart
• Investigate drawing or hover issues

Build charts with TradingView's lightweight-charts, including candlesticks, lines, live updates, scales, and annotations. Guidance checks installed types and v5 APIs to support chart integration, framework lifecycle handling, and troubleshooting of common data and display issues.

• Build candlestick charts with a separate volume pane
• Add live updates and historical data
• Fix v4-to-v5 API migration issues

Create masks that identify object regions in images using points, boxes, or existing masks. The skill guides automatic mask generation, transparent-background extraction, annotation workflows, and deployment, without requiring training for each specific task.

• Extracting objects with transparent backgrounds
• Building annotation tools with point and box selection
• Generating object masks automatically

Build Vue 3 applications using JavaScript and JSDoc comments that describe data types. Create components and reusable logic, configure Vite, routing, and state management, and check annotations and behavior with ESLint and Vitest.

• Build Vue 3 interfaces using JavaScript
• Add JSDoc type hints to components and shared logic
• Migrate Vue 2 Options API code to Composition API

Build Python 3.11+ applications with type annotations, asynchronous operations, and structured error handling. The skill also creates pytest tests and checks code with mypy, black, and ruff to support consistent implementation and validation.

• Add type annotations and strict type checking
• Implement asynchronous network or file operations
• Create pytest tests with fixtures and mocks