「discovery」の検索結果

Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published CFD score (SpCas9-only, relative ranker) or MIT/CRISTA/energy models, runs variant-aware screening against gnomAD/individual genomes (CRISPRme), and frames the empirical genome-wide discovery assays (GUIDE-seq, CIRCLE-seq, CHANGE-seq, DISCOVER-seq, Digenome-seq) and high-fidelity nuclease choice (HiFi Cas9, Sniper-Cas9, eSpCas9, SpCas9-HF1). Use when assessing guide RNA specificity, choosing among candidate guides, screening a therapeutic guide against population variation, or planning empirical off-target validation. Distinguishes predicted vs detected vs validated. On-target activity scoring and deaminase (Cas-independent) base/prime-editor off-targets are separate skills.

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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

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Run the advanced iterative workflow — Wayfinding AST discovery, Relentless Grilling, contract and spec design, TDD, council review, and docs.

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Map owned assets, attack surface, and inventory for systems the requester is authorized to assess. Use for asset discovery, service catalogs, and exposure reviews — never unauthorized scanning.

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Azure API Center SDK for .NET. Centralized API inventory management with governance, versioning, and discovery.

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Find and evaluate influencers for brand partnerships, verify authenticity, and track collaboration performance across Instagram, Facebook, YouTube, and TikTok.

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Semantic + keyword search and connection-discovery across the user's own Apple Notes via the apple-notes MCP server. Use when the user wants to find, recall, or synthesize something from their notes, or surface non-obvious bridges/related notes. macOS, on-device.

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Provide comprehensive techniques for testing REST, SOAP, and GraphQL APIs during bug bounty hunting and penetration testing engagements. Covers vulnerability discovery, authentication bypass, IDOR exploitation, and API-specific attack vectors.

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Entry point for new work. Determines the best action path or work decomposition (update existing spec, create new spec, mixed decomposition, or no spec needed) and refines ideas through structured dialogue.

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Design an approval-gated feature specification from approved requirements. Use when PWDEV Flow discovery is complete and the user needs architecture decisions, component boundaries, quality constraints, and a definition of done.

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Expert guidance for integrating and building applications with shadcn/ui components, including component discovery, installation, customization, and best practices.

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Orchestrates legacy AEM (6.x, AMS, on-prem) to AEM as a Cloud Service migration using BPA CSV or cache, CAM/MCP target discovery, and one-pattern-per-session workflow. Use for BPA/CAM findings, Cloud Service blockers, or fixes for scheduler, ResourceChangeListener, replication, EventListener, OSGi EventHandler, DAM AssetManager, HTL data-sly-test lint. OSGi configs → Cloud Manager — scan ui.config, .cfg.json, secrets, $[secret:]/$[env:] — agent follows references/osgi-cfg-json-cloud-manager.md when prompted. Transformation steps live in the best-practices skill—read it and the right references/ modules before editing code.

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Orchestrator for the pre-decision business-idea lifecycle — generate ideas, model them, evaluate them, validate them with customers, and only then hand off to product-soul / brainstorming. Routes through `idea-generation`, `business-modeling`, `idea-evaluation`, and `customer-discovery`. Load when the user asks to explore business ideas, find a startup idea, evaluate a venture, validate an idea, says "what business should I start", "should I build this", "is this a good business", "I have a startup idea", "evaluate this venture", "model this business", "validate this idea", "Mom Test this", "Lean Canvas this", "Business Model Canvas", "Value Proposition Canvas", "go/no-go on this idea". Pre-decision suite — once one idea is committed, hands off to `product-soul`. Does NOT design features (use `brainstorming`) or audit built products (use `reality-check`).

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Run a structured discovery interview and produce a complete, developer-ready Product Requirements Document. Load when the user asks to write a PRD, create product requirements, document a feature, define user stories with acceptance criteria, or turn a rough idea into a formal product requirements document. Also triggers on "document this feature", "write requirements for", "create a one-pager", "turn this into a PRD", "I need a PRD for", or any request to produce a structured product document for stakeholder alignment or engineering handoff. Supports Full PRD, Lean PRD, and One-Pager formats. Note: for executable feature specifications (FRs, NFRs, ACs as Given/When/Then consumable by AI coding agents), route to `feature-spec` instead — PRDs frame the product, feature-specs encode the implementable contract.

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。

A skill that creates new Claude skills and automatically shares them on Slack using Rube for seamless team collaboration and skill discovery.

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。

Azure API Center SDK for .NET. Centralized API inventory management with governance, versioning, and discovery.

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。

Provide comprehensive techniques for testing REST, SOAP, and GraphQL APIs during bug bounty hunting and penetration testing engagements. Covers vulnerability discovery, authentication bypass, IDOR exploitation, and API-specific attack vectors.

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。

Find and evaluate influencers for brand partnerships, verify authenticity, and track collaboration performance across Instagram, Facebook, YouTube, and TikTok.

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。

Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.

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。

Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published CFD score (SpCas9-only, relative ranker) or MIT/CRISTA/energy models, runs variant-aware screening against gnomAD/individual genomes (CRISPRme), and frames the empirical genome-wide discovery assays (GUIDE-seq, CIRCLE-seq, CHANGE-seq, DISCOVER-seq, Digenome-seq) and high-fidelity nuclease choice (HiFi Cas9, Sniper-Cas9, eSpCas9, SpCas9-HF1). Use when assessing guide RNA specificity, choosing among candidate guides, screening a therapeutic guide against population variation, or planning empirical off-target validation. Distinguishes predicted vs detected vs validated. On-target activity scoring and deaminase (Cas-independent) base/prime-editor off-targets are separate skills.

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。