「discover」の検索結果

Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDTA (plant/structural TEs), or EarlGrey (auto-curating wrapper), and quantifies TE expression from RNA-seq with TEtranscripts/SQuIRE. Covers de-novo-library-as-curation-project, soft-vs-hard masking, the domesticated-gene over-masking massacre, Dfam-vs-RepBase, TE classification (Class I/II, family-vs-copy), Kimura repeat landscapes, LAI, and the RNA-seq multimapping problem. Use when masking repeats before gene prediction, building a TE library for a non-model genome, or analyzing transposable-element content or expression.

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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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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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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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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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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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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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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.

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Ranks eligible skill candidates with explicit retrieval evidence, capability coverage, and uncertainty. NOT for discovery, authorization, or execution planning.

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OpenLineage, DataHub, Marquez for data lineage tracking and impact analysis. Activate on: data lineage, OpenLineage, DataHub, Marquez, impact analysis, data catalog, column lineage, data discovery. NOT for: data quality validation (use data-quality-guardian), dbt documentation (use dbt-analytics-engineer).

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Matches natural language task descriptions to appropriate skills using semantic similarity. Handles fuzzy matching, intent extraction, and capability alignment. Activate on 'find skill', 'match task', 'semantic search', 'skill lookup', 'what skill for'. NOT for ranking matches (use dag-capability-ranker) or skill catalog (use dag-skill-registry).

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Full-site crawling, scraping, and site mapping via Firecrawl MCP. Use when user says "crawl site", "map site", "full crawl", "find all pages", "broken links", "site structure", "discover pages", "JS rendering", or needs site-wide analysis.

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Pipeline that turns a big system idea into briefs for an agent fleet. Use when Arman says 'let's plan out X', 'build or overhaul the X system', 'create the vision and plan for X', 'do the full discovery process', 'get this ready for a fleet', or 'do what we did for education', or when carrying forward a VISION, COMPETITIVE_INSIGHTS, roadmap, or briefs doc. NOT for one feature in a live system (use build-sub-feature).

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Discovery batch that grows the Provider Access Launch queue. Use when asked to find more user-connected OAuth, API, API-key, remote MCP, marketplace, or partner-access campaigns for a capability, provider family, MCP/plugin catalog, or competitive gap. NOT for client Local Listings distribution.

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Create an Agent SKILL.md fallback for an existing find-XXXX finder that relies on a fragile discovery foundation — above all LLM_DECOMPILE (patterns C/D/E), which matches the decompiled shape of a predecessor function against a stored reference and breaks when a symbol is inlined or de-inlined in a way the reference does not cover. The generated fallback coexists with the preprocessor and runs only when it returns failure, recovering every target robustly by decompiling the predecessor and following the inline/de-inline boundary with semantic anchors. Use when a finder broke on a game update, or you want to durably backstop one before it does. The recipe generalizes to any finder foundation. Triggers: create agent skill fallback, add SKILL.md fallback, robust fallback for finder, backstop LLM_DECOMPILE finder, final guarantee skill

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Convert an existing find-XXXX SKILL.md into a preprocessor Python script, updating configs/<GAMEVER>.yaml and removing the old SKILL.md. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns.

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Create a new find-XXXX preprocessor Python script from scratch (no existing SKILL.md), add configs/<GAMEVER>.yaml skill and symbol entries. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns. Use when a GitHub issue or user instruction specifies a new function to find.

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Helps users discover and install agent skills. Use when they ask "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities with installable skills.

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Generative Engine Optimization for AI search engines (ChatGPT, Claude, Perplexity). Use when improving how content is discovered and cited by AI assistants.

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Academic paper search across 14+ scholarly platforms including arXiv, PubMed, Google Scholar, Web of Science, Semantic Scholar, Sci-Hub, and more. Use for literature review, research discovery, and citation management.

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Index-based file discovery using ABOUTME headers. Use INSTEAD of grep or Explore agent when searching for files by purpose or feature. Faster and more accurate than scanning code. Invoke this skill when user asks "which files handle X", "where is Y implemented", or when you need to find files related to a feature or task.

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Executive coaching skill that helps you plan your 2026 using research-backed process goals. Guides you through discovery questions, creates outcome goals, converts them to daily behaviors, and sets up accountability systems. Use when you want to plan your year, set goals, or need a coach to help you stay focused.

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。