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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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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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Parses Kubernetes API server audit logs (JSON lines) to detect exec-into-pod, secret access, RBAC modifications, privileged pod creation, and anonymous API access. Builds threat detection rules from audit event patterns. Use when investigating Kubernetes cluster compromise or building k8s-specific SIEM detection rules.
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Focused Signals scout for PostHog setup health. Reads the project's active health issues — the deterministic findings of PostHog's own health checks (no live events, outdated SDKs, missing reverse proxy, absent web vitals, ingestion warnings, failing data-warehouse models, and more) — and decides which are genuinely worth surfacing. Unlike a one-signal-per-issue push, it bundles kind-clusters into a single finding, weights by real blast radius (cross-referencing actual event volume and reach), and prioritizes issues an agent can resolve via the MCP. Emits only above the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other skills.
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Focused Signals scout for PostHog projects using error tracking. Watches `$exception` bursts, stuck loops, multi-fingerprint clusters, status regressions, and stack-trace activity-name patterns. Emits findings only when they clear the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other skills.
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Focused Signals scout for PostHog projects using AI observability. Rotates through a set of lenses — cost, latency, errors, volume, eval performance, eval/enrichment config, clusters, and tool usage — watching each for trends and spikes sliced by the dimensions it discovers over time. Leans on the sandbox's bundled `exploring-llm-*` deep-dive skills for the actual queries. Emits findings only when they clear the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other scouts.
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Focused Signals scout for PostHog projects using session replay. Watches two promises the replay product makes: that sessions are actually being recorded (capture integrity — recording volume vanishing while site traffic doesn't), and that the friction evidence inside recordings gets seen (rage-click / dead-click clusters concentrating on a page or element, error-after-interaction cohorts, recurring replay vision themes nobody aggregates). Emits findings only when they clear the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet.
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Focused Signals scout for PostHog projects running surveys. Watches active surveys for score regressions (NPS / CSAT / rating drops), response-volume drops, abandonment spikes, and targeting drift, AND aggregates open-text responses into recurring themes the team should know about (clusters of complaints, praise, feature requests). Emits findings only when a theme or anomaly clears the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other skills.
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Monte Carlo simulation for statistical mechanics — Ising model, Metropolis-Hastings, Wolff cluster algorithm, observables (magnetization, susceptibility, specific heat), finite-size scaling, and critical phenomena analysis.
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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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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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Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with explicit out-of-distribution and label-transfer uncertainty. Use when annotating new single-cell datasets against a pre-trained reference, deciding which mapping method fits, or judging whether transferred labels are trustworthy. For de novo clustering and manual annotation see single-cell/cell-annotation; for batch integration without a reference see single-cell/batch-integration.
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Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
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End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.
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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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ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.
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UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
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Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA, rWikiPathways), and visualize. Use when a DESeq2/edgeR/limma result must become enriched GO terms, KEGG/Reactome/WikiPathways pathways, or a GSEA leading edge; when the input is a full ranking for all genes (GSEA, named decreasing vector) or only a pre-selected list (ORA plus a defensible background universe); or when assembling DE-to-pathway end to end. The DE list and ranking statistic come from differential-expression/de-results; per-method nuance lives in the pathway-analysis skills.
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This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
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Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.
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Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
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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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Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
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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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