“annotation”的搜索结果

Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Quantitative agent evaluation using 4-metric framework (correctness/step_ratio/tool_call_ratio/latency_ratio) with ideal trajectory annotation and capability-categorical taxonomy. Use when measuring agent efficiency, comparing agent variants, or gating new agents through correctness→efficiency phases. Complements harness-eval (SE benchmarks) and evaluator-optimizer (qualitative rubric).

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Report the health of the central system spec at `docs/system/` across seven checks — coverage gaps, stale elements, dangling anchors, duplicate anchors, orphan shards, unillustrated elements, and shards missing their kind annotation. Report-first and read-only: it repairs nothing until a human confirms a specific item. Use when the corpus has drifted, after a merge that touched `docs/system/`, or from `/archive` Step 5.5 in report-only mode. Requires `memory.architecture_map.enabled`.

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Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.

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Create a simple, modern HTML review page and run a local browser feedback loop with inline element/text annotations and structured questions. Use when the user wants to discuss or iterate on a design, plan, comparison, scope decision, content draft, or other topic that is easier to review visually than in chat.

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Use when creating a new Laravel API endpoint — Controller, FormRequest, Resource, route, Policy, OpenAPI annotations — versioned route layout, single-action `__invoke` controllers.

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Transforms data into compelling visual narratives by applying narrative structure, annotation techniques, scrollytelling patterns, and honest framing to data journalism, presentations, and infographics. Use when creating data-driven articles or reports, designing infographics with narrative, building scrollytelling experiences, annotating charts to guide interpretation, or when user mentions data storytelling, presentation design, annotated chart, narrative visualization.

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NYT-discipline data visualization. Applies the design rules of The New York Times graphics desk + Upshot — color, typography, annotation, chart-type selection — to make any chart render at Times grade. Use whenever generating charts, dashboards, reports, or data-driven webpages. Triggers: "make this chart look professional", "NYT style", "editorial chart", "data viz", "dashboard design".

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Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.

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Read the latest Glassbox code review and apply all feedback annotations

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Recast a supplied everyday photo as a witty illustrated product instruction sheet with a large Chinese title and concise English annotations. Use for 日常说明书、宠物使用说明、生活物品冷幽默说明图 or a fictional everyday object manual poster.

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Register WordPress Abilities: machine-readable plugin operations with JSON Schema contracts, required permission callbacks, optional REST exposure, and AI/MCP-friendly discovery. Covers categories, wp_register_ability, WP_Ability::execute, REST run endpoints, meta.show_in_rest, annotations, and Ability vs REST route vs custom hook decisions. Use when exposing plugin functionality to agents, admin JS, external tools, or reviewing AI integration code.

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Generate hand-drawn 16:9 article illustrations with the Grav character IP, sparse annotations, and absurd but clear visual metaphors.

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Enable nullable reference types in a C# project and systematically resolve all warnings. USE FOR: adopting NRTs in existing codebases, file-by-file or project-wide migration, fixing CS8602/CS8618/CS86xx warnings, annotating APIs for nullability, cleaning up null-forgiving operators, upgrading dependencies with new nullable annotations. DO NOT USE FOR: projects already fully migrated with zero warnings (unless auditing suppressions), fixing a handful of nullable warnings in code that already has NRTs enabled, suppressing warnings without fixing them, C# 7.3 or earlier projects. INVOKES: Get-NullableReadiness.ps1 scanner script.

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Make .NET projects compatible with Native AOT and trimming by systematically resolving IL trim/AOT analyzer warnings. USE FOR: making projects AOT-compatible, fixing trimming warnings, resolving IL warnings (IL2026, IL2070, IL2067, IL2072, IL3050), adding DynamicallyAccessedMembers annotations, enabling IsAotCompatible. DO NOT USE FOR: publishing native AOT binaries, optimizing binary size, replacing reflection-heavy libraries with alternatives. INVOKES: no tools — pure knowledge skill.

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MCP server documentation conventions for high-quality generated skills. Use when writing tool descriptions, `_meta` annotations, or input schemas for MCP extraction.

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