「cluster」の検索結果

Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.

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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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End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.

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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.

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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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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Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.

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Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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ESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai1-structure-prediction or boltz-structure-prediction. For QC thresholds, use protein-design-qc.

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ESM2 protein language model for embeddings and sequence scoring. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai or boltz. For QC thresholds, use protein-qc.

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Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.

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Runtime per-test healing with evidence: multi-attribute selector healing, environment-aware diagnosis, flake classification, quarantine management, and confidence-scored auto-repair. Goes beyond simple locator fallbacks to cover action-level healing, data healing, and observable repair workflows. Use when: "flaky test," "test stability," "self-healing locator," "broken locator recovery," "unreliable test," "quarantine flaky test." Not for: bulk regenerating selectors after a planned UI refactor — use selector-drift-recovery (this skill heals ONE test at runtime; that one rewrites many tests offline). Not for: classifying/clustering CI failures into bug reports — use ai-bug-triage. Related: playwright-automation, selector-drift-recovery, ci-cd-integration, qa-metrics, ai-bug-triage.

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Audit a whole regression suite and prune/restructure it with evidence: per-test coverage fingerprinting, AST near-duplicate clustering, CI-history mining for never-failing and flaky tests, prune decision rules (redundant/obsolete/low-value/keep), smoke/core/extended tiering by risk and defect-detection history, and a defensible "what we deleted and why" record. Deletion is destructive — quarantine and human sign-off are mandatory. Use when: "audit the test suite," "prune redundant tests," "find duplicate tests," "which tests can we delete," "restructure into smoke/core/extended," "is this test pulling its weight," "shrink the regression suite." Not for: Judging whether an individual test is WELL-WRITTEN (smells, assertions) — that is ai-qa-review. Healing one flaky test at runtime — that is test-reliability. Bulk selector regeneration after a UI refactor — that is selector-drift-recovery. Related: ai-qa-review, coverage-analysis, test-reliability, risk-based-testing, qa-project-context.

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Hybrid fingerprint + LLM pipeline for bug classification, deduplication, and ticket generation. Normalizes CI logs, creates stable fingerprints, clusters near-duplicates, then uses LLM for severity classification and ticket writing. Includes bug reporting templates and severity/priority matrix. Use when: "bug triage," "classify bugs," "failure analysis," "auto-classify," "CI failures," "bug report," "defect template." Not for: runtime self-healing of one flaky locator — use test-reliability. Not for: designing new tests from production telemetry — use observability-driven-testing. Related: qa-metrics, qa-dashboard, ci-cd-integration, qa-project-context.

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Expert guidance for CapRover, the open-source PaaS that turns any Linux server into a Heroku-like platform with automatic HTTPS, one-click app deployment, and Docker-based containerization. Helps developers deploy applications, configure custom domains, and manage the CapRover cluster.

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cert-manager for automatic TLS certificate management in Kubernetes. Use when the user needs to issue, renew, and manage TLS certificates from Let's Encrypt or other CAs, configure ClusterIssuers, and secure Ingress resources.

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Kubernetes is the operating system for the cloud. It schedules containers, handles networking, manages storage, and keeps your apps running. But K8s has a steep learning curve - abstractions on abstractions on abstractions. This skill covers the core concepts (Pods, Deployments, Services), production patterns (health checks, resource limits, HPA), and the gotchas that catch everyone (namespace confusion, service discovery, secret management). 2025 reality: You probably don't need to run your own cluster. Use managed K8s (EKS, GKE, AKS) unless you have a very good reason not to. Focus on writing good manifests, not managing etcd. Use when "kubernetes, k8s, kubectl, deployment manifest, helm chart, kustomize, pod, service yaml, ingress, horizontal pod autoscaler, hpa, kubernetes, k8s, containers, orchestration, devops, cloud-native, helm, kustomize" mentioned.

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World-class Kubernetes operations - deployments, debugging, Helm charts, and the battle scars from managing clusters that serve millions of requestsUse when "kubernetes, k8s, kubectl, helm, pod, deployment, service, ingress, configmap, secret, statefulset, daemonset, hpa, pvc, crashloopbackoff, imagepullbackoff, oomkilled, liveness probe, readiness probe, kubernetes, k8s, containers, docker, helm, deployment, devops, cloud-native" mentioned.

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World-class content strategy expertise combining the frameworks of Andy Crestodina's data-driven approach, Ann Handley's "everybody writes" philosophy, and the content engines that power companies like HubSpot, Ahrefs, and Intercom. Content strategy isn't about creating content - it's about creating the right content for the right audience at the right time in the right format. The best content strategists think in systems, not pieces. They build content engines that compound over time and turn strangers into customers and customers into advocates. Use when "content strategy, content plan, editorial calendar, blog strategy, content marketing, topic clusters, pillar content, content audit, content calendar, SEO content, content distribution, content funnel, thought leadership, content engine, content topics, what to write, content, strategy, editorial, SEO, blog, planning, distribution, measurement" mentioned.

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Brian Dean (Backlinko 创始人) 视角. Content-driven SEO 派代表. Skyscraper Technique + Pillar Cluster + 长内容 + 链接建设. 调用此 skill 时, 用 Brian Dean 框架做 SEO 决策.

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Pre-change blast-radius report for a symbol or file. Walks tree-sitting references, augments with a plain-text scan over non-parsed files (configs, plain docs), and clusters affected sites by feature (`_FEATURES.md`) or top-level package. Use when about to refactor, rename, or delete something in a repo you don't own — "what breaks if I change `validateUser`", "who calls this", "is this safe to remove", "where is this used", "blast radius", "impact analysis". This is the CONVERGENT pre-change risk skill — for "what is this repo?" use exploring-codebases; for "where is X?" use searching-codebases.

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Blog strategy development including topic cluster architecture with hub-and-spoke design, audience mapping, competitive landscape analysis, AI citation surface strategy across ChatGPT/Perplexity/AI Overviews, distribution channel planning (YouTube, Reddit, review platforms for GEO), content scoring targets, measurement framework, and content differentiation through original research and first-hand experience. Use when user says "blog strategy", "content strategy", "blog positioning", "what should I blog about", "blog topics", "content pillars", "blog ideation".

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Organize qualitative research data into an affinity diagram with themes, clusters, and insight statements. Use when synthesizing large amounts of qualitative data from interviews, observations, or surveys.

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