「cluster」の検索結果

Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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。

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 (Than 2008) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012). 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.

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。

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.

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。

Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.

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。

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) with SES scaling, 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.

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。

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, MHFP6 LSH forest, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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。

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/MntJULiP/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.

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。

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.

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。

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.

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。

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.

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。

Help with MongoDB query optimization and indexing. Use only when the user asks for optimization or performance: "How do I optimize this query?", "How do I index this?", "Why is this query slow?", "Can you fix my slow queries?", "What are the slow queries on my cluster?", etc. Do not invoke for general MongoDB query writing unless user asks for performance or index help. Prefer indexing as optimization strategy. Use MongoDB MCP when available.

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。

This skill should be used when user asks to "query Azure resources", "list storage accounts", "manage Key Vault secrets", "work with Cosmos DB", "check AKS clusters", "use Azure MCP", or interact with any Azure service.

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。

Connect MATLAB to Databricks via Spark (Databricks Connect) or JDBC (Database Toolbox). Use when setting up the MATLAB Interface for Databricks, configuring authentication (OauthU2M, OauthM2M, PAT), creating Spark sessions with getDatabricksSession(), reading Unity Catalog tables with server-side filtering, creating JDBC connections with databricks.JDBCConnection or StandaloneJDBCConnection, connecting to SQL Warehouses, selecting JDBC drivers (Simba/OSS), or writing data back to Databricks. Triggers on: Databricks Connect, Spark from MATLAB, getDatabricksSession, .databrickscfg, databricks.JDBCConnection, StandaloneJDBCConnection, SQLWarehouse, Databricks JDBC, Databricks cluster, large table server-side filtering.

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。

AWS ECS container orchestration for running Docker containers. Use when deploying containerized applications, configuring task definitions, setting up services, managing clusters, or troubleshooting container issues.

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。

Implement Kubernetes security contexts, Pod Security Standards, and network policies. Secure cluster components and workloads. Use when hardening Kubernetes deployments or meeting security compliance.

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。

Use service mesh patterns for AI inference traffic management, mTLS, canary releases, policy enforcement, and cross-cluster resilience.

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。

Configure Redis for caching and data storage. Set up clustering, persistence, and Sentinel. Use when implementing Redis caching or queues.

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。

Operate GPU-backed Kubernetes clusters for AI inference and training with scheduling, autoscaling, node health, MIG partitioning, and cost controls.

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。

Deploy and manage Azure Kubernetes Service clusters. Configure node pools, networking, and integrations. Use when running Kubernetes workloads on Azure.

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。

Manage Red Hat OpenShift clusters and deployments. Configure projects, routes, builds, and deploy applications using OpenShift-specific features. Use when working with OpenShift Container Platform or OKD for enterprise Kubernetes.

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。

Auto-scale LLM inference clusters on Kubernetes using KEDA, custom GPU metrics, and horizontal pod autoscaling. Handle traffic spikes, implement queue-based scaling, and optimize cost with spot instances for AI workloads.

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。

Deploy and manage Google Kubernetes Engine clusters. Configure node pools, networking, and workload identity. Use when running Kubernetes on GCP.

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。

Amazon review authenticity analyzer. Detect fake reviews, suspicious patterns, and rating manipulation. Includes time clustering detection, content similarity analysis, rating distribution checks, and verified purchase validation. Progressive analysis with L1-L4 depth levels. No API key required.

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。

eBay review and feedback authenticity analyzer. Detect fake reviews, suspicious seller feedback patterns, and buyer manipulation. Includes time clustering detection, content similarity analysis, and eBay-specific red flag identification. No API key required.

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。