「annotation」の検索結果

InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell comm

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Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including

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'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

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This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources

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Provides multi-school trading Q&A, chart/OHLCV analysis, annotation, and fresh-market workflows covering ICT/SMC, ChanLun, Wyckoff, Price Action, Order Flow, VSA, and Elliott Wave. Use for trading concepts; capability-discovery questions about available analysis lenses, Schools, models, modes, or data sources; attached charts; pasted OHLCV; chart annotation; or asset-plus-timeframe requests across crypto, stocks, or forex. Defaults unselected market analysis to strict ICT/SMC, honors explicit School/source selectors, and fails closed when no native analyzer exists. Phase 1 comparison is Q&A-only; fetch fresh Mobius Quant API data only after the capability gate.

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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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Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.

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Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.

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Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. Use when running BUSCO QC, comparing assemblies, or reporting completeness. See also: prokka-genome-annotation for annotation workflows feeding BUSCO.

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Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores. Use for UCSC annotations; Ensembl REST API for Ensembl gene IDs and VEP variant annotation.

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Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.

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Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.

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Operate CVAT for computer-vision annotation, dataset workflows, SDK/CLI automation, auto-annotation, and self-hosted deployment.

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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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End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.

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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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Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when automatically annotating cell types using reference datasets.

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Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.

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図面 JSON を検証し、A3 の PDF / SVG と注釈一覧を生成して設計レビューの候補を返す。図面レビュー、寸法確認、注釈作成、drawing review、annotation に使う。

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

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Parse all `# implements:` annotations in source code and emit `library/_code-index.md` as a shelf-index. Also extracts cross-module import edges and writes `library/_dependency-edges.md`. Idempotent — re-running produces byte-identical output if no annotations or imports changed.

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Use this agent when you need to synthesize and distill the core functions of a gene from multiple information sources (textual summaries, reviewed annotations, bioinformatics analysis) and populate the `core_functions` section of a gene review YAML file. This agent should be called after completing the gene research, annotation review, and bioinformatics analysis phases of a gene review project.

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Use this agent when you need to review UniProt annotation rules (ARBA, UniRule) for quality, biological accuracy, and GO annotation appropriateness. This agent performs comprehensive analysis of rule condition sets, evaluates literature support, assesses taxonomic scope, and recommends curation actions.

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Use this agent when you need to perform custom bioinformatics analyses on genes or proteins that go beyond standard database lookups. This includes situations where existing domain/family annotations from UniProt are insufficient, when you need to verify dubious annotations, or when you need to perform comparative analyses across gene sets. The agent creates reproducible analysis pipelines with proper dependency management and documentation.

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