「annotations」の検索結果

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma, Schwede & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2021 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma, Schwede & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2021 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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。

Annotate screenshots, diagrams, and images with callout rectangles, arrows, labels, and color-coded highlights using PIL. Includes rules for animated GIF annotations with timing and pacing.

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Creates and manages annotation configs (categorical, continuous, freeform label schemas) and annotation queues (human review workflows) on Arize. Applies human annotations to project spans via the Python SDK. Use when the user mentions annotation config, annotation queue, label schema, human feedback, bulk annotate spans, update_annotations, labeling queue, annotate record, or human review.

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Build forms, validate data, and react to user input in Blazor. USE FOR adding forms, search boxes, filter panels, inline editing, data-entry UI, file uploads, validation (annotations or custom), handling form submissions, and binding input controls. Covers EditForm, built-in input components, DataAnnotationsValidator, custom validation, SSR form patterns (SupplyParameterFromForm, FormName, AntiforgeryToken, Enhance), and @bind for simple interactive controls. DO NOT USE for project scaffolding (see create-blazor-project) or prerendering issues (see support-prerendering).

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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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Queries S3 object metadata, tracks bucket activity, audits object changes, searches annotations, and analyzes storage metrics using S3 Metadata system tables (journal, inventory, annotation) and S3 Storage Lens tables via Athena SQL. Applies when counting objects, finding recent uploads or deletions, identifying who wrote to a prefix, breaking down storage classes, finding objects by tag, searching annotation content, analyzing storage lens metrics, or enabling S3 Metadata tracking. Prefers system tables over raw S3 APIs (list-objects-v2, head-object) at scale. Trigger phrases: bucket activity, object count, who uploaded, track deletions, storage class breakdown, find by tag, search annotations, storage lens metrics, audit bucket changes.

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Process filler word annotations to generate video edit lists. Use when working with timestamp annotations for removing speech disfluencies (um, uh, like, you know) from audio/video content.

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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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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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Display 3-D image volumes, medical image volumes, surface meshes, and annotations for 3-D image processing. Use when displaying 3-D images or isosurfaces with volshow, creating volume viewers with viewer3d, adding Regions of Interest (ROI) or annotations, overlaying masks or segmentations, streaming volumetric data, or building apps with volume display.

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Display images and annotations for image processing, computer vision, and visual inspection. Use when displaying images with imageshow, creating image viewers with viewer2d, adding Regions of Interest (ROI) or annotations, overlaying masks or segmentations, streaming video frames, or building apps with image display.

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Build forms, validate data, and react to user input in Blazor. USE FOR adding forms, search boxes, filter panels, inline editing, data-entry UI, file uploads, validation (annotations or custom), handling form submissions, and binding input controls. Covers EditForm, built-in input components, DataAnnotationsValidator, custom validation, SSR form patterns (SupplyParameterFromForm, FormName, AntiforgeryToken, Enhance), and @bind for simple interactive controls. DO NOT USE for project scaffolding (see create-blazor-project) or prerendering issues (see support-prerendering).

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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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Generate formal specifications including preconditions, postconditions, invariants, and contracts from code or requirements. Use this skill when documenting APIs, creating formal verification annotations, defining function contracts, specifying class invariants, writing design-by-contract code, or preparing code for formal verification. Supports multiple specification languages including JML, ACSL, Dafny, Eiffel contracts, and documentation annotations.

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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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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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Requires detailed type annotations for all Python functions, methods, and class members.

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。