「annotation」の検索結果

Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

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Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

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Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNOG-mapper (orthology), InterProScan (domain signatures), and KofamScan (KEGG), routing specialized functions to dbCAN/antiSMASH/AMRFinderPlus/SignalP. Covers the orthology-vs-domain-vs-homology paradigms, the annotation-error percolation cascade, domain-presence-is-not-function, GO IEA circularity in enrichment, evidence tiering, and bit-score/coverage thresholds. Use when adding functional annotation to predicted genes, choosing between eggNOG-mapper and InterProScan, or judging how much to trust a functional label.

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Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Expert in 3D computer vision labeling tools, workflows, and AI-assisted annotation for LiDAR, point clouds, and sensor fusion. Covers SAM4D/Point-SAM, human-in-the-loop architectures, and vertical-specific training strategies. Activate on '3D labeling', 'point cloud annotation', 'LiDAR labeling', 'SAM 3D', 'SAM4D', 'sensor fusion annotation', '3D bounding box', 'semantic segmentation point cloud'. NOT for 2D image labeling (use clip-aware-embeddings), general ML training (use ml-engineer), video annotation without 3D (use computer-vision-pipeline), or VLM prompt engineering (use prompt-engineer).

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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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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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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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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 "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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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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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.

日本語の概要は準備中です。原文の説明を表示しています。