Data Science & ML Agent Skills

UniProt Protein Database Access

Accesses the UniProt REST API to perform comprehensive protein searches, sequence retrieval, and cross-database identifier mapping.

KEGG Bioinformatics Database

Accesses the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API for biological pathway analysis and molecular interaction mapping.

FDA Regulatory Data Access

Queries the openFDA API to retrieve comprehensive data on drugs, medical devices, foods, and regulatory actions for safety research and analysis.

GWAS Catalog Database

Queries the NHGRI-EBI GWAS Catalog to retrieve genetic variants, SNP-trait associations, and comprehensive genomic summary statistics.

NCBI GEO Database Integration

Accesses and processes NCBI Gene Expression Omnibus (GEO) datasets for transcriptomics and functional genomics analysis.

Denario Autonomous Research

Automates the end-to-end scientific research pipeline from initial hypothesis generation to publication-ready LaTeX manuscripts.

COSMIC Cancer Database Access

Accesses and queries the Catalogue of Somatic Mutations in Cancer (COSMIC) to retrieve genomic data, mutational signatures, and cancer gene census information.

UniProt Database Integration

Enables seamless programmatic access to UniProt for protein sequence retrieval, functional annotation, and biological database ID mapping.

ToolUniverse Scientific Research Skill

Accesses over 600 scientific tools and datasets to automate research workflows across bioinformatics, genomics, and drug discovery.

NeuroKit2 Biosignal Analysis

Processes and analyzes physiological signals including ECG, EEG, and EDA for psychophysiology research and clinical applications.

Matplotlib Data Visualization

Generates publication-quality static, animated, and interactive visualizations using Python's foundational plotting library.

ETE Toolkit for Phylogenetics

Manipulates, analyzes, and visualizes phylogenetic trees with support for evolutionary event detection and NCBI taxonomy integration.

deepTools NGS Analysis

Processes and visualizes high-throughput sequencing data (NGS) including ChIP-seq, RNA-seq, and ATAC-seq workflows.

Biopython Molecular Biology

Performs advanced biological computation and molecular biology workflows using the Biopython toolkit.

Paper2All Academic Transformer

Transforms academic papers into interactive websites, professional presentation videos, and print-ready conference posters.

Scientific Peer Review & Evaluation

Evaluates scientific manuscripts and grant proposals using systematic methodology, statistical rigor, and ethical standards.

Scikit-learn Machine Learning

Streamlines the implementation, evaluation, and deployment of classical machine learning models using the scikit-learn library.

TorchDrug Machine Learning

Facilitates machine learning for drug discovery using a PyTorch-based toolkit for molecular property prediction, protein modeling, and retrosynthesis.

Scanpy Single-Cell Analysis

Performs comprehensive single-cell RNA-seq analysis workflows including quality control, clustering, and cell type annotation.

UMAP Machine Learning

Performs fast nonlinear dimensionality reduction and manifold learning for high-dimensional data visualization and clustering.

BioServices

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

Polars Data Analysis

Enables high-performance data manipulation and analysis using the Polars DataFrame library's lightning-fast expression API.

Hypogenic Scientific Hypothesis Engine

Accelerates scientific discovery by automatically generating, testing, and refining hypotheses from datasets and research literature using LLMs.

Geniml Genomic ML

Applies machine learning to genomic interval data for training region embeddings, analyzing scATAC-seq, and building consensus peak universes.

Scikit-bio Bioinformatics Toolkit

Analyzes biological data using specialized tools for sequence manipulation, phylogenetics, and microbial ecology metrics.

scikit-bio Bioinformatics Toolkit

Processes and analyzes biological data using scikit-bio for sequence alignment, phylogenetics, and microbiome diversity studies.

OMERO Microscopy Data Management

Integrates Claude with the OMERO platform to manage, analyze, and automate bioimaging data workflows using the Python API.

SICMUtils (Emmy) Computational Physics

Provides a comprehensive Clojure library for symbolic mathematics, automatic differentiation, and classical mechanics simulation based on SICM concepts.

COBRApy Metabolic Modeling

Performs constraint-based metabolic modeling and systems biology simulations using the COBRApy Python library.

Stable Baselines3 RL

Implements reinforcement learning workflows using Stable Baselines3 for training agents, creating environments, and optimizing deep RL models.