551 件 ・ 関連度順
概要と使いどころ
Predict protein-coding genes in eukaryotic genomes using BRAKER3 for combined RNA-seq and protein evidence, or GALBA for protein-only evidence. Runs Augustus with trained parameters for accurate gene models. Use when annotating a newly assembled eukaryotic genome or improving existing gene predictions.
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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
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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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Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.
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。
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.
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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.
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。
End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.
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Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), 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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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.
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。
ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.
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Structure retrieval, confidence-aware AlphaFold DB usage, coordinate download, PAE and pLDDT interpretation, and structure-guided biological annotation.
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。
Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".
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。
Workflow for small-variant and structural-variant discovery, filtering, annotation, and interpretation from sequencing data.
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。
Workflow for untargeted or targeted metabolomics including preprocessing, normalization, annotation, statistics, and pathway mapping.
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。
Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.
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。
Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.
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Extracts executable task definitions from Markdown files and runs them as shell pipelines. Parses fenced code blocks with task metadata annotations and manages dependencies between tasks.
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Portrait Mode for SVGs — foveated vectorization with 4-zone selective detail. Combines vision annotations, MediaPipe segmentation/landmarks, and optional saliency. Like phone portrait mode, but vectorized. Use when vectorizing a portrait or photo where subject detail should outrank background detail.
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。
Specify wireframe layouts with content priority, component placement, and annotation.
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Suede AI MCP release QA, scoped to this pack's own server (mcp/suede-skills-mcp.mjs) and its catalog, install, and docs surface. Runs the full JSON-RPC lifecycle against a live server (initialize, notifications/initialized, ping, tools/list, tools/call, resources/list, resources/read, prompts/list, prompts/get), plus protocol negotiation, closed input and output schemas, tool annotations, structuredContent with text fallbacks, malformed-input probes, clean stdio, catalog-to-folder agreement, and install-path language. Use when the MCP server, mcp/catalog.json, a tool, resource, or prompt definition, or the MCP install docs change, or before publishing an MCP release. A check that did not run against the live server is a FAIL, not a skip. NOT FOR: a generic third-party MCP server, which this skill's hardcoded surface does not describe; fixing or testing the public install path itself (use suede-launch-packaging).
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Use when building Spring Boot applications with Neo4j using Spring Data Neo4j (SDN 7.x/8.x) — @Node entity mapping, @Relationship, @RelationshipProperties, Neo4jRepository, ReactiveNeo4jRepository, @Query annotations, application.yml configuration, projections, Neo4jClient, Neo4jTemplate, transactions, auditing, or Spring AI Neo4jVectorStore vector search. Does NOT handle raw Java driver code without Spring — use neo4j-driver-java-skill. Does NOT handle Cypher query authoring — use neo4j-cypher-skill. Does NOT handle driver version upgrades — use neo4j-migration-skill.
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。
Design a structured protocol for auditing AI-generated text against Ennis's six CT standards. Use when students need to critically evaluate AI output in any subject.
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。
Register and implement PydanticAI tools with proper context handling, type annotations, and docstrings. Use when adding tool capabilities to agents, implementing function calling, or creating agent actions.
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RIPDPI Compose performance: stability annotations, compiler metrics, LazyColumn key/contentType, per-screen recomposition notes. Use when diagnosing recomposition, stability, or list performance here.
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