「annotation」の検索結果

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Use this skill when a driver needs to edit their own ELD record. Covers what edits are allowed, what edits trigger annotations, the unassigned-driving-time procedure, and when carriers must accept or reject driver edits.

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Analyze development-set disagreements between human annotations and one Coval text LLM judge, then propose a focused prompt revision. Use coval-calibrate-metric for independent trust measurements.

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Adds accessibility annotations (ARIA labels, roles, alt text) to make web content accessible. Use when user asks to "add accessibility", "make accessible", "add aria labels", "wcag compliance", or "screen reader support".

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Complete guide for AutoFixture advanced customization techniques. Use when you need to customize AutoFixture builders or handle special type test data generation rules. Covers DataAnnotations automatic integration, ISpecimenBuilder implementation, priority management. Includes DateTime/numeric range builders, generic design, and fluent extension methods. Keywords: autofixture customization, autofixture customize, autofixture customization, specimen builder, ISpecimenBuilder, RandomDateTimeSequenceGenerator, NumericRangeBuilder, DataAnnotations autofixture, fixture.Customizations, Insert(0), custom builder, NoSpecimen, generic builder

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[BETA] AEM Cloud Service expert skill — migrate javax.inject.@Inject fields in Sling Model (@Model) classes to injector-specific annotations (@ValueMapValue / @OSGiService / @SlingObject). Self-discoverable (scan for @Model classes with field-level @Inject); the replacement is chosen deterministically from each field's declared type. Use for "fix @Inject in HeroModel.java", "modernize my Sling Models", or when scanning an AEM project for @Inject misuse. Detailed decision table, companion-annotation handling, import management, and file-level skip policy are in recipe.md. This skill is in beta. Verify all outputs before applying them to production projects.

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MyBatisを使うJavaのデータ保存・取得処理を設計、レビューします。SQLと結果の対応付け、動的SQLの安全性、トランザクションや検索性能を扱います。

• マッパーとXMLの対応付けの設計
• 動的SQLと入力値の安全性確認
• 複数更新のトランザクション確認

A crisp greybox / blueprint lo-fi wireframe — neutral grey blocks on a pale page, image placeholders drawn as a rectangle with a diagonal X, text shown as solid "lorem bars" of varying widths, sharp 1.5–2px borders, and a single monospace redline accent for annotations. Reads like a structural blueprint before any visual design is applied. Use when the brief asks for "greybox", "blueprint wireframe", "lo-fi dashboard", "low fidelity", "线框图", or "灰盒原型".

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A hand-drawn wireframe exploration — graph-paper background, marker / pencil tone, multiple tab labels for variants, sticky-note annotations, scribbled chart placeholders, hatched fills. Reads like a designer's whiteboard before any pixels are committed. Use when the brief asks for "wireframe", "sketch wireframe", "hand-drawn", "lo-fi", "whiteboard", "草稿", or "手绘原型".

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A lo-fi multi-screen MOBILE flow wireframe — three or four phone frames laid out in a row on a board, showing a connected user flow (Onboarding → Home feed → Item detail → Confirm). Grey-box content inside each device, dashed connector arrows + numbered step labels between screens, and a couple of annotation callouts. Reads like an app flow pinned to a whiteboard before any pixels are committed. Use when the brief asks for "mobile wireframe", "app flow", "user flow wireframe", "lo-fi mobile", "low fidelity", "线框图", "移动端线框", or "App 流程".

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An annotated / redline lo-fi wireframe — a desktop landing/marketing page drawn as flat greyboxes inside a browser chrome frame, overlaid with numbered annotation pins (①②③④⑤) in a single accent color, paired with a right-hand SPEC PANEL that lists each numbered pin with a short engineering / UX note. This is the "wireframe + redline spec" style — clean, flat, low-fidelity, NOT hand-drawn. Use when the brief asks for "annotated wireframe", "redline wireframe", "wireframe with spec", "lo-fi landing wireframe", "low fidelity", "线框图", "标注线框", or "redline".

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Command-line interface for Openscreen — a screen recording editor. A stateful CLI for editing screen recordings with zoom, speed ramps, trim, crop, annotations, and polished exports. Built on the Openscreen JSON project format with ffmpeg as the rendering backend. Designed for AI agents and power users who need programmatic video editing.

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Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty; use scanpy for standard preprocessing and exploratory analysis.

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Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".

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Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.

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Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.

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Searches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and returns results with reproducible provenance. Covers PubMed, PMC, Europe PMC, bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall, OpenCitations, PubTator3, Zenodo, Figshare, ROR, BioStudies, and DOAJ. Use when searching for papers, citations, DOI/PMID/arXiv lookups, abstracts, full text, open-access PDFs, preprints, citation graphs, author publications, biomedical entity annotations, deposited records (Zenodo, Figshare, BioStudies), institution ROR IDs, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X", "look up this DOI", "who cites this paper", or "get me the PDF".

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Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrations. Use for reproducible biological data curation or a LaminDB lakehouse.

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Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use this skill for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.

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Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

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