「cluster」の検索結果

Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Use when users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

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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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Reserved and on-demand GPU cloud instances for ML training and inference. Use when you need dedicated GPU instances with simple SSH access, persistent filesystems, or high-performance multi-node clusters for large-scale training.

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Facebook's library for efficient similarity search and clustering of dense vectors. Supports billions of vectors, GPU acceleration, and various index types (Flat, IVF, HNSW). Use for fast k-NN search, large-scale vector retrieval, or when you need pure similarity search without metadata. Best for high-performance applications.

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Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.

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Complete SEO + GEO (Generative Engine Optimization) system for SaaS companies wanting to rank on both Google and AI search engines (ChatGPT, Perplexity, Gemini, Claude). Use this skill whenever the user asks about SEO strategy, keyword research, content planning, writing SEO-optimized articles, auditing their search performance, creating a content calendar, analyzing competitors, or optimizing for AI search visibility. Trigger on: "seo", "keyword research", "content calendar", "rank on google", "search traffic", "write an article", "blog post", "serp", "backlinks", "competitor analysis", "content cluster", "seo audit", "geo optimization", "ai search", "search console", "organic traffic", "content strategy", "publish article", "seo setup", "ranking", "impressions", "ctr", "meta description", "schema markup", "faq schema". Also trigger when a user wants to set up their SaaS blog SEO from scratch, analyze their current rankings, or create a publishing workflow.

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Deprecated redirect skill that routes legacy 'content creator' requests to the correct specialist. Use when a user invokes 'content creator', asks to write a blog post, article, guide, or brand voice analysis (routes to content-production), or asks to plan content, build a topic cluster, or create a content calendar (routes to content-strategy). Does not handle requests directly — identifies user intent and redirects to content-production for writing/SEO/brand-voice tasks or content-strategy for planning tasks.

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Manage the Matrix/Virgo-Core Proxmox VE cluster (nodes Foxtrot, Golf, Hotel - MINISFORUM MS-A2 with AMD Ryzen 9 9955HX). Covers VM provisioning, VLAN networking, CEPH storage, and automation via Python (proxmoxer), Ansible (community.general.proxmox), and Terraform (Telmate/proxmox).

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Comprehensive MCP tool reference for Proxmox Virtual Environment management - 92 tools across 14 domains including QEMU VMs, LXC containers, cluster operations, storage, networking, Ceph, certificates, ACME, and notifications

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Administers Proxmox VE hosts, creates and manages VMs with qm, manages LXC containers with pct, configures storage, networking, clusters, and automates provisioning tasks via the Proxmox CLI.

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Expert Proxmox VE automation using the community.proxmox Ansible collection for VM provisioning, template management, and cluster operations with minimal CLI usage.

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Facebook's library for efficient similarity search and clustering of dense vectors. Supports billions of vectors, GPU acceleration, and various index types (Flat, IVF, HNSW). Use for fast k-NN search, large-scale vector retrieval, or when you need pure similarity search without metadata. Best for high-performance applications.

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Reserved and on-demand GPU cloud instances for ML training and inference. Use when you need dedicated GPU instances with simple SSH access, persistent filesystems, or high-performance multi-node clusters for large-scale training.

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。

Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.

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Creates comprehensive content outlines and topic clusters for SEO. Plans content calendars and identifies topic gaps. Use PROACTIVELY for content strategy and planning.

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Apply bottom-up and top-down role mining techniques to discover optimal RBAC roles from existing user-permission assignments, reducing role explosion and enforcing least privilege.

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Analyze the threat landscape using MISP (Malware Information Sharing Platform) by querying event statistics, attribute distributions, threat actor galaxy clusters, and tag trends over time. Uses PyMISP to pull event data, compute IOC type breakdowns, identify top threat actors and malware families, and generate threat landscape reports with temporal trends.

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