Skill UI

This script performs statistical analysis on Zeek connection logs (conn.log) to detect Command and Control (C2) beaconing patterns. It leverages the ZAT library to load data into Pandas DataFrames, calculates inter-arrival time statistics, and flags connections with low standard deviation relative to the mean. This technique is crucial for network threat hunting and security incident investigation when identifying malicious, periodic callbacks.

This skill provides a comprehensive workflow to transform raw data into professional visual charts. It intelligently analyzes data features (e.g., trends, comparisons, flows) to select the optimal chart type (line, bar, pie, etc.). Users provide data and specifications, and the skill generates a high-quality, detailed chart image using a structured JavaScript process.

This skill enhances research query formulation by translating vague, colloquial, or generalized descriptions into precise, standard academic terminology. When initial search terms are broad (e.g., "conjugal happiness"), this technique suggests multiple plausible academic synonyms (e.g., "marital satisfaction," "relationship quality"). By improving the precision of the search query and incorporating structured constraints (like keywords, years, or sample sizes), it significantly boosts the relevance and effectiveness of academic paper retrieval.

Infers candidate gene regulatory networks from bulk or single-cell expression data using GRNBoost2 and GENIE3 algorithms. Ranks transcription factor-target associations with Dask-compatible parallel execution, sparse expression support, and network stability validation for biological research applications.

Programmatically query the CZ CELLxGENE Census for versioned single-cell and spatial transcriptomics data, including population-scale cell metadata, gene expression slices, summary counts, source H5AD URIs, embeddings, and reference atlas comparisons.

Pythonic wrapper around RDKit for drug discovery workflows: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, and parallel batch processing. Returns native RDKit Mol objects.

LaminDB is an open-source lineage-native lakehouse designed for biological datasets and models. It enables queryable, traceable, and validated data management across various storage formats like S3 and Postgres. Users can track computational workflows, curate data with ontologies via Bionty, and ensure FAIR compliance. Ideal for managing scRNA-seq, spatial transcriptomics, and integrating ML pipelines while maintaining reproducibility and collaboration.

Python bindings to OpenMS for computational mass spectrometry. Analyze proteomics and metabolomics LC-MS/MS data: feature detection, peptide and protein identification, label-free and isobaric quantification, adduct and accurate-mass annotation, plus ready-to-run workflow scripts.

Python cheminformatics toolkit for fine-grained molecular control: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D coordinate generation, similarity, reactions, and visualization.

Compile verified scholarly evidence and references for scientific manuscripts or research briefs. Runs multi-pass Parallel Search with Extract source verification, ranked deduplication, and optional Research/Chat backends to deliver a manuscript-ready research packet targeting 60 unique references.

Scanpy is a scalable Python toolkit for single-cell RNA-seq analysis, covering quality control, normalization, dimensionality reduction, clustering, and visualization. It supports converting R formats to h5ad and includes ready-to-run CLI scripts for end-to-end workflows, making it ideal for exploratory scRNA-seq analysis and publication-quality plotting.

This skill covers using the SHAP library to explain and audit machine learning predictions. It guides users on selecting explainers, computing feature attributions, and validating results. It includes workflows for local and global visualizations, handling multi-output models, and ensuring model behavior descriptions are accurate without implying causality. Requires Python 3.12+ and specific SHAP versions.