Data Science & ML Agent Skills

Molfeat Molecular Featurization

Simplifies molecular featurization by providing access to over 100 pre-trained embeddings and hand-crafted featurizers for machine learning.

NetworkX Graph Analysis

Provides a comprehensive toolkit for creating, manipulating, and analyzing complex network structures and graph algorithms in Python.

Scientific Literature Review

Conducts systematic, multi-database literature searches and synthesizes research findings into professionally formatted documents with verified citations.

Pysam Genomics Toolkit

Processes genomic datasets including sequence alignments, variants, and reference sequences using a Pythonic interface to htslib.

Adaptyv Protein Design

Automates protein sequence optimization and experimental validation through a cloud-based wet-lab platform.

Medicinal Chemistry Toolkit

Applies medicinal chemistry filters, drug-likeness rules, and structural alerts for molecular prioritization in drug discovery.

LaSalle Invariance Stability Analysis

Analyzes the asymptotic stability of dynamical systems using the LaSalle Invariance principle to determine long-term qualitative behavior.

ClinVar Genomic Database

Queries and interprets NCBI ClinVar genetic variant data to provide clinical significance classifications and genomic annotations.

Dask Parallel Computing

Scales Python data workflows across multiple cores and machines for larger-than-RAM datasets using parallel and distributed computing.

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.

Scikit-Survival for Python

Implements advanced survival analysis and time-to-event modeling using the scikit-survival library in Python.

Vaex Big Data Processing

Enables high-performance analysis and visualization of tabular datasets with billions of rows using lazy, out-of-core DataFrames.

Scikit-learn Machine Learning

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

NCBI GEO Database Integration

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

UniProt Database Integration

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

Matplotlib Data Visualization

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

PyTDC (Therapeutics Data Commons)

Provides AI-ready datasets, benchmarks, and molecular oracles for drug discovery and therapeutic machine learning.

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.

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.

KEGG Bioinformatics Database

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

Paper2All Academic Transformer

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

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.

ETE Toolkit for Phylogenetics

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

Scikit-bio Bioinformatics Toolkit

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

COBRApy Metabolic Modeling

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

Polars Data Analysis

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

PyDESeq2 RNA-seq Analysis

Performs robust differential gene expression analysis on bulk RNA-seq data using the PyDESeq2 framework.