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Prepare single-cell or single-nucleus RNA-seq analysis by checking inputs and selecting workflows that turn FASTQ sequencing files into count matrices. Route quality checks, cell annotation, clustering, and UMAP visualization to the embedded downstream skill.
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Guides single-cell RNA-seq analysis, which examines gene activity in individual cells. Covers data loading, quality checks, clustering, marker genes, cell type annotation, and plots, with AnnData handling and scVI/scANVI workflow planning.
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Analyze time series, observations ordered over time, using aeon in Python. Build classification, prediction, and clustering workflows, detect unusual patterns or changes, and compare methods through an interface compatible with scikit-learn.
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Build or refresh a browser-viewable topic graph over Claude session history using local clustering. Use for mapping or clustering sessions, recent or stale topic analysis, or rebuilding/showing the session graph. Unlike wiki-history-ingest, it indexes raw sessions and never writes to the vault.
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Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.
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Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.
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Build unified multi-level category taxonomy from hierarchical product category paths from any e-commerce companies using embedding-based recursive clustering with intelligent category naming via weighted word frequency analysis.
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SERP-based semantic topic clustering for content architecture planning. Groups keywords by actual Google SERP overlap (not text similarity), designs hub-and-spoke content clusters with internal link matrices, and generates interactive visualizations. Optionally executes content creation if claude-blog is installed. Use when user says "topic cluster", "content cluster", "semantic clustering", "pillar page", "hub and spoke", "content architecture", "keyword grouping", or "cluster plan".
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Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.
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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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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.
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SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.
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Map 50-200+ keywords into topical clusters for SEO domination. Build content roadmaps for topical authority. Triggers on: "keyword research", "keyword clustering", "topical authority", "keyword map", "keyword strategy", "content roadmap for SEO", "keyword grouping", "topic clusters", "SEO keyword plan", "map my keywords", "keyword cluster", "hub and spoke content", "build topical authority", "SEO content plan", "keyword universe".
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Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.
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Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.
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SERP-based semantic topic clustering for content architecture planning. Groups keywords by actual Google SERP overlap (not text similarity), designs hub-and-spoke content clusters with internal link matrices, and generates interactive visualizations. Optionally executes content creation if claude-blog is installed. Use when user says "topic cluster", "content cluster", "semantic clustering", "pillar page", "hub and spoke", "content architecture", "keyword grouping", or "cluster plan".
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Cluster a list of keywords into topical groups with search intent labels, validated search volume, KD, and CPC data. Use this skill whenever a user provides a list of keywords (pasted, uploaded as CSV/Excel, or via Google Sheet URL) and asks to cluster, group, map, organize, or categorize them. Also trigger when a user says "keyword cluster", "cluster my keywords", "group these keywords", "keyword map", "keyword strategy from this list", "organize keywords by topic", or pastes or uploads a list of keywords and wants structure from it. Always use this skill — do not attempt keyword clustering manually without following this workflow.
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Build unified multi-level category taxonomy from hierarchical product category paths from any e-commerce companies using embedding-based recursive clustering with intelligent category naming via weighted word frequency analysis.
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教師なし分析と EDA 前処理（欠測 / 欠損 / NaN / 補完 / imputation / 外れ値処理、クラスタリング / セグメンテーション / k-means / 階層クラスタリング / GMM / DBSCAN、次元削減 / PCA / 主成分分析 / 因子分析 / UMAP / t-SNE、異常検知 / anomaly detection / 不正検知）を実行したら必ずセットで出す図と値のルーター。fillna, dropna, fill_null, SimpleImputer, IterativeImputer, missingno, KMeans, AgglomerativeClustering, DBSCAN, GaussianMixture, silhouette_score, dendrogram, PCA, FactorAnalysis, calculate_kmo, TSNE, umap.UMAP, IsolationForest, LocalOutlierFactor, pyod がコードに現れたとき、またはユーザーが「欠損を埋めて」「クラスタリングして」「主成分で 要約して」「異常を検知して」「データをきれいにして」と言ったときに使う。安定性・k の根拠・平行分析・ベースラインに 言及がなくても適用する。SKILL.md のルーティング表で手法を特定し、対応する references/<手法>.md を読んでから実行する。 教師あり予測は predictive-modeling-diagnostics、回帰・検定は statistical-inference-diagnostics を使う。
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Customer feedback analysis — sentiment detection, NPS/CSAT frameworks, feature request clustering, support ticket triage, churn signal detection, and feedback-to-roadmap translation
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Tracks adversary C2 and staging infrastructure by clustering indicators on shared attributes (TLS/JARM, certificate fields, favicon hashes, ASN, registration patterns) to find related hosts. Activates for requests to track adversary infrastructure, cluster C2 servers, or pivot on infrastructure attributes to find related hosts.
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Computes cryptographic and fuzzy fingerprints for malware samples: MD5/SHA-1/SHA-256 for exact identity, plus import hashing (imphash), section hashing, and fuzzy hashes (ssdeep, TLSH) to cluster related variants. Activates for requests to hash a sample, compute imphash, or fingerprint files for similarity clustering.
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Build face recognition systems with InsightFace, ArcFace, enrollment pipelines, HDBSCAN clustering, and privacy-compliant architecture. Activate on: face recognition, face enrollment, face clustering, identity verification, facial search. NOT for: general object detection (computer-vision-pipeline), emotion analysis (ai-engineer).
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Snowflake, BigQuery, clustering, partitioning, and materialized views for warehouse performance. Activate on: Snowflake, BigQuery, Redshift, query optimization, clustering, partitioning, materialized view, warehouse cost, query profile. NOT for: dbt model structure (use dbt-analytics-engineer), data modeling (use dimensional-modeler).
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