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Build custom browser charts with D3, including precise labels, annotations, zooming, and range selection. Create SVG graphics that adapt to mobile screens, use meaningful contextual backgrounds, and support export when needed.
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Design a dark monochrome interface around an exploded 3D wireframe, an outline view of separated parts. Coordinate annotations, connector lines, typography, and small metric displays to explain product structures or system states.
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Prepare .NET projects for Native AOT, compilation before execution, and trimming, which removes unused code. Use build warnings to guide type annotations, reflection changes, and source-generated JSON serialization, then check all target frameworks.
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Search saved Zotero papers by keywords or meaning, read selected PDF pages, and organize references. Use shell commands to update bibliographic details, tags, notes, and annotations, add items by identifier, and export bibliographies.
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Create or edit element annotations in desktop Browser tabs, or update saved annotation comments through the plugin RPC.
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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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Create and customize MATLAB charts and plots. Plot types (line, scatter, bar, histogram, heatmap, surface), axes configuration, annotations, data tips, interactive plots, animation, multiple axes with tiledlayout, colororder, and performance optimization. Works for standalone figures, Live Scripts, and uifigure apps. Use when plotting data, customizing axes, adding annotations or interactivity, animating charts, or arranging multiple axes. Triggers: plot, chart, graph, axes, uiaxes, annotation, data tips, animation, tiledlayout, colororder, heatmap, scatter, figure, visualization, export.
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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
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Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.
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Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.
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Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.
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Cell type annotation strategy for scRNA-seq: name clusters manually from canonical markers, transfer labels from a reference (CellTypist, popV), or do both and validate one against the other. Covers matching tissue and developmental stage, marker evidence, annotation confidence, doublets, unresolved clusters. Use when planning or troubleshooting how to annotate cells.
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Create ACSL (ANSI/ISO C Specification Language) formal annotations for C/C++ programs. Use this skill when working with formal verification, adding function contracts (requires/ensures), loop invariants, assertions, memory safety annotations, or any ACSL specifications. Supports Frama-C verification and generates comprehensive formal specifications for C/C++ code.
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Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.
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This skill should be used when the user encounters "no-untyped-def" mypy errors, asks to "fix no-untyped-def errors", "add type annotations to functions", or mentions "Function is missing a type annotation". Provides specific workflow for fixing missing type annotations while respecting forbidden type constraints.
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This skill should be used when the user encounters "var-annotated" mypy errors, asks to "fix var-annotated errors", "add type annotations to variables", or mentions "Need type annotation for" errors. Provides workflow for fixing missing variable type annotations while respecting forbidden type constraints (no Any, dict[str, Any], list[Any], etc.).
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Analyze an arbitrary codebase to auto-detect workflows, data pipelines, and file dependencies using putior's put_auto() engine. Produces an annotation plan that maps detected I/O patterns to source files across 30+ supported languages with 902 auto-detection patterns. Use when onboarding onto an unfamiliar codebase to understand data flow, starting putior integration in a project without existing annotations, auditing a project's data pipeline before documentation, or preparing an annotation plan before running annotate-source-files.
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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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Use this agent when you need to systematically review existing GO annotations for a gene and make curation decisions based on literature evidence and functional analysis. This agent should be called after seeding the SPECIES/GENE/GENE-ai-review.yaml file, which seeds each annotation with `action: PENDING`; these should all be manually reviewed.
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Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact on regulatory elements, perform enrichment testing of variant sets in tissue-specific annotations, or link variants to target genes through enhancer-gene maps. Handles the full post-GWAS workflow from variant set → tissue mapping → functional annotation → fine-mapping awareness → enrichment → variant-to-gene → prioritization. Use this skill for ANY variant interpretation task involving ENCODE chromatin, accessibility, TF binding, or 3D genome data.
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Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build overlap for ENCODE regions, convert coordinates between GRCh37 and GRCh38, resolve gene IDs (Ensembl ↔ symbol ↔ RefSeq), look up gene phenotype associations, or cross-reference ENCODE targets with Ensembl annotations. Also use when the user mentions Ensembl, VEP, variant effect predictor, liftover, assembly conversion, regulatory build, gene lookup, or cross-references between databases.
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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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Expert en annotation de données avancé (annotation, quality, active learning, consensus, tools)
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