Data Science & ML Agent Skills

ClinVar Genomic Analysis

Queries the NCBI ClinVar database to retrieve, interpret, and process human genetic variant classifications and clinical significance.

Scholar Evaluation Framework

Evaluates scholarly research and academic papers using the structured ScholarEval methodology for rigor and quality.

Aeon Time Series ML

Implements advanced time series machine learning tasks including forecasting, classification, and anomaly detection using a scikit-learn compatible framework.

SimPy Simulation Framework

Builds process-based discrete-event simulations in Python to model complex systems like manufacturing, logistics, and network traffic.

Datamol Cheminformatics

Simplifies molecular cheminformatics workflows with a Pythonic wrapper for RDKit, featuring structure standardization, descriptor calculation, and 3D conformer generation.

COBRApy Metabolic Modeling

Performs constraint-based reconstruction and analysis of metabolic models for systems biology and metabolic engineering.

DNAnexus Genomics Integration

Streamlines genomic data management and bioinformatics app development on the DNAnexus cloud platform using the dxpy Python SDK.

Genomic Tools and Algorithms in Rust (Gtars)

Simplifies high-performance genomic interval analysis and machine learning preprocessing using Rust-powered toolsets.

UMAP Dimensionality Reduction

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

PDB Structural Biology Database

Accesses and retrieves 3D protein and nucleic acid structures from the RCSB PDB for structural biology and drug discovery research.

Pymoo Optimization

Solves complex single and multi-objective optimization problems using evolutionary algorithms and Pareto front analysis.

Pysam Genomic Data Processing

Processes and analyzes high-throughput sequencing data including SAM, BAM, VCF, and FASTA files using a Pythonic interface to htslib.

KEGG Scientific Database Access

Accesses the KEGG REST API for biological pathway analysis, gene mapping, and metabolic network research.

PubMed Database Access

Facilitates advanced biomedical literature searches and programmatic data retrieval from the PubMed database using MeSH terms and E-utilities.

SymPy Symbolic Mathematics

Performs exact symbolic mathematical computations including algebra, calculus, and equation solving using the SymPy Python library.

Histolab Pathology Processing

Automates digital pathology workflows by processing whole slide images, detecting tissue regions, and extracting informative tiles for deep learning pipelines.

LaminDB Biological Data Framework

Manages biological datasets with automated lineage tracking, ontology-based validation, and FAIR data principles through a unified Python API.

Biomni Biomedical Research Agent

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

PyOpenMS Mass Spectrometry Analysis

Analyzes mass spectrometry data for proteomics and metabolomics using the OpenMS Python interface.

NeuroKit2 Biosignal Processing

Processes and analyzes complex physiological signals including ECG, EEG, EDA, and respiratory patterns for research and clinical applications.

FluidSim CFD Simulations

Simulates complex fluid dynamics using Python-based high-performance solvers for Navier-Stokes, shallow water, and stratified flows.

MarkItDown Document Converter

Converts diverse file formats including PDFs, Office documents, and media into LLM-optimized Markdown while preserving structural integrity.

UniProt Protein Database

Accesses the UniProt REST API to retrieve protein sequences, functional annotations, and map identifiers across biological databases.

ETE Toolkit for Phylogenetics

Manipulates, analyzes, and visualizes phylogenetic and hierarchical trees for genomic research and clustering analysis.

Transformers for AI & ML

Integrates Hugging Face Transformers for advanced natural language processing, computer vision, and audio tasks.

ClinicalTrials.gov Explorer

Queries the ClinicalTrials.gov API to search, filter, and analyze global clinical study data for medical research and patient matching.

deepTools NGS Analysis

Facilitates high-throughput sequencing data analysis, visualization, and quality control for genomics workflows.

BioServices Bioinformatics

Accesses over 40 bioinformatics web services and databases for biological data retrieval and analysis within Python workflows.

Statsmodels Statistical Analysis

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

Statistical Analysis Toolkit

Performs comprehensive statistical hypothesis testing, regression analysis, and Bayesian modeling with automated assumption checking and APA-style reporting.