Data Science & ML Agent Skills

Metabolomics Workbench Explorer

Accesses the NIH Metabolomics Workbench REST API to retrieve comprehensive metabolomics study data, metabolite structures, and standardized RefMet nomenclature.

LangGraph v1 & LangChain Assistant

Facilitates the development and migration of Python-based AI agents using LangGraph v1 and LangChain v1 standards.

Whisper Audio Transcription

Transcribes audio files locally using whisper.cpp with CUDA acceleration for high-performance speech-to-text conversion.

Data Visualization Creator

Transforms raw datasets into professional-grade charts, graphs, and visual plots using intelligent data analysis.

Pymoo Optimization Framework

Optimizes complex multi-objective and constrained problems using state-of-the-art evolutionary algorithms and decision-making tools.

PufferLib Reinforcement Learning

Accelerates reinforcement learning workflows with high-performance environment vectorization and optimized PPO training.

Scanpy Single-Cell Analysis

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

HMDB Metabolome Database

Accesses and queries the Human Metabolome Database for detailed metabolite information, clinical biomarkers, and biochemical pathways.

LabArchives ELN Integration

Automates electronic lab notebook workflows including data uploads, notebook backups, and programmatic entry management via the LabArchives REST API.

MATLAB & Octave Scientific Computing

Provides specialized support for MATLAB and GNU Octave numerical computing, matrix operations, and scientific visualization.

Bioinformatics & Genomic Analysis (pysam)

Processes genomic data files including SAM, BAM, VCF, and FASTA using a high-performance Python interface to htslib.

Stable Baselines3 RL Suite

Implements production-ready reinforcement learning algorithms using a unified, scikit-learn-style API for efficient agent training and evaluation.

DrugBank Database Integration

Accesses and analyzes comprehensive pharmaceutical data, including drug properties, interactions, molecular targets, and chemical structures from DrugBank.

Hypogenic Scientific Hypothesis Discovery

Automates scientific hypothesis generation and testing from tabular datasets using LLMs and literature integration.

K-Dense Scientific Research Bridge

Connects Claude Scientific Skills with the K-Dense Web platform to handle complex, multi-agent scientific research workflows.

SHAP Model Interpretability

Explains machine learning model predictions and feature importance using Shapley Additive exPlanations for transparent AI.

ClinicalTrials.gov Search & Integration

Queries the ClinicalTrials.gov API v2 to search, filter, and extract comprehensive clinical research data and trial details.

ClinPGx Pharmacogenomics Database

Queries gene-drug interactions, clinical guidelines, and genetic variant annotations from the ClinPGx database for precision medicine applications.

Geniml: Genomic Machine Learning

Builds machine learning models and embeddings for genomic interval data to enable similarity searches, clustering, and single-cell analysis.

PyDESeq2 Gene Analysis

Performs differential gene expression analysis for bulk RNA-seq data using Python-based DESeq2 workflows.

PyTorch Geometric (PyG)

Develops and trains Graph Neural Networks (GNNs) using the PyTorch Geometric library for irregular data structures and geometric deep learning.

Media Understanding & Analysis

Analyzes and extracts insights from images, videos, and audio files using advanced AI models.

KEGG Database Connector

Provides direct access to the KEGG REST API for biological pathway analysis, gene mapping, and metabolic research.

PyTorch Lightning

Streamlines deep learning development by organizing PyTorch code into scalable, boilerplate-free Lightning modules and automated training workflows.

ETE Phylogenetic Toolkit

Provides comprehensive tools for phylogenetic tree manipulation, evolutionary analysis, and high-quality biological data visualization.

Scientific Critical Thinking

Evaluates scientific research rigor and evidence quality using standardized frameworks like GRADE and Cochrane.

Python Project Structure Refactor

Transforms monolithic Python research code and notebooks into modular, production-ready package structures.

SimPy Simulation Engine

Builds process-based discrete-event simulations in Python to model complex systems with resource contention and time-based events.

Embedding & Chunking Strategies

Optimizes vector search and RAG applications through intelligent embedding model selection and advanced document chunking strategies.

Gemini Audio Integration

Implements comprehensive audio processing and text-to-speech generation using the Google Gemini API.