Data Science & ML Agent Skills

Statsmodels Statistical Analysis

Performs rigorous statistical modeling, econometric analysis, and hypothesis testing using Python's statsmodels library.

PyTorch Lightning

Organizes and scales PyTorch deep learning workflows by automating training loops, hardware orchestration, and boilerplate code.

COBRApy Metabolic Modeling

Facilitates constraint-based reconstruction and analysis (COBRA) of metabolic models for systems biology and metabolic engineering.

PathML

Analyzes whole-slide pathology images and multiparametric imaging data using computational tools for tissue segmentation, spatial graphs, and machine learning.

NCBI Gene Database Tools

Queries and retrieves genomic data from NCBI Gene databases using E-utilities and the modern Datasets API.

AlphaFold Database Access

Facilitates the retrieval and analysis of over 200 million AI-predicted protein structures from the AlphaFold DB for biological research and drug discovery.

Exploratory Data Analysis Toolkit

Automates comprehensive statistical analysis and visual profiling for diverse datasets to uncover hidden patterns, anomalies, and actionable insights.

scvi-tools

Empowers single-cell omics analysis with deep generative models for dimensionality reduction, batch correction, and multimodal data integration.

HuggingFace Model Inference

Provides procedural guidance for setting up HuggingFace model inference services using Flask, covering environment setup, model caching, and robust API implementation.

Pymoo Optimization

Implements advanced multi-objective and many-objective optimization frameworks using state-of-the-art evolutionary algorithms and Pareto analysis.

Dask Parallel Computing

Enables parallel and distributed computing in Python to scale pandas and NumPy operations beyond memory limits.

PyDESeq2 Gene Expression Analysis

Identifies differentially expressed genes from bulk RNA-seq counts using the PyDESeq2 statistical framework.

TorchDrug Scientific Computing

Accelerates drug discovery and molecular research by providing specialized tools for graph neural networks, protein modeling, and chemical property prediction.

Transformers

Integrates state-of-the-art machine learning models for NLP, computer vision, and audio tasks using the Hugging Face ecosystem.

Medchem Molecular Filters

Applies medicinal chemistry rules and structural alerts to triage and prioritize compound libraries for drug discovery workflows.

ESM Protein Modeling

Provides advanced protein language models for generating novel sequences, predicting structures, and creating high-quality embeddings for protein engineering and scientific research.

Matplotlib Visualization Expert

Generates professional, publication-quality Python visualizations including line plots, heatmaps, and 3D charts using the Matplotlib library.

Histolab Digital Pathology

Processes whole slide images (WSI) for digital pathology by automating tissue detection, tile extraction, and preprocessing for computational pipelines.

LLM Project Development

Builds production-grade LLM applications using structured pipelines, task-model fit analysis, and deterministic architecture patterns.

RDKit Cheminformatics

Enables advanced molecular modeling, chemical property calculation, and structural analysis within Python workflows.

Aeon Time Series Toolkit

Builds and deploys machine learning models for complex time series tasks like forecasting, classification, and anomaly detection.

BioServices Bioinformatics Toolkit

Provides programmatic access to over 40 bioinformatics web services for biological data retrieval, identifier mapping, and pathway analysis.

ReportLab PDF Generation

Automates the creation of professional PDF documents, reports, and invoices using the robust ReportLab Python toolkit.

ML Model Leaderboard Navigator

Provides systematic guidance for identifying, verifying, and extracting current performance data from machine learning benchmarks and embedding leaderboards.

DiffDock Molecular Docking

Predicts high-accuracy 3D binding poses for protein-ligand complexes using diffusion-based deep learning models.

gget Bioinformatics Toolkit

Provides unified access to 20+ genomic databases and bioinformatics tools for gene information, sequence analysis, and protein structure prediction.

Polars High-Performance Data Analysis

Optimizes data processing workflows using the high-performance Polars DataFrame library and expression API.

Semantic PDF Research

Indexes PDF document collections using LightRAG to enable semantic search and context-aware research within Claude Code.

Pysam Bioinformatics Toolkit

Simplifies genomic data processing by providing a Pythonic interface for reading, writing, and manipulating SAM, BAM, CRAM, and VCF files.

Biomni

Executes autonomous multi-step biomedical research tasks including genomics analysis, drug discovery, and clinical interpretation.