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Astropy Astronomy Toolkit

K-Dense-AI/claude-scientific-skills

Astropy delivers a comprehensive Python toolkit for astronomy workflows, covering units, celestial coordinates, FITS files, cosmological models, precise time handling, tables, and WCS transformations for research or data pipelines.

Benchling Integration Toolkit

benchling-integration

K-Dense-AI/claude-scientific-skills

Automate Benchling R&D workflows through the Python SDK or REST API, handling registries, inventory, ELNs, workflows, and data warehouse queries with secure auth for lab data integration.

Biopython Molecular Toolkit

K-Dense-AI/claude-scientific-skills

Biopython is a comprehensive Python toolkit for molecular biology, offering sequence manipulation, file I/O, NCBI database access, BLAST automation, structure parsing, phylogenetics, and motif analytics; ideal for building bioinformatics pipelines and batch processing workflows.

BioServices API Gateway

K-Dense-AI/claude-scientific-skills

BioServices API Gateway provides unified Python interfaces across 40+ bioinformatics services like UniProt, KEGG, ChEMBL, and Reactome, enabling cross-database queries, identifier mapping, pathway and sequence analysis within a single workflow.

ChEMBL Bioactivity Query

chembl-database

K-Dense-AI/claude-scientific-skills

Programmatically query ChEMBL bioactive molecules, targets, and approved drugs via the Python client; filter by structure, properties, activities, and indications to support inhibitor hunting or SAR studies for medicinal chemistry.

COBRApy Metabolic Modeling

K-Dense-AI/claude-scientific-skills

COBRApy is a Python library for constraint-based reconstruction and analysis of metabolic networks, offering SBML-compatible model loading/saving, FBA/FVA optimization, genetic or reaction knockouts, flux sampling, and production envelope analysis for systems biology and metabolic engineering.

Data Commons Client

datacommons-client

K-Dense-AI/claude-scientific-skills

Provides a Python client for querying the Data Commons knowledge graph so teams can resolve entities, fetch statistical observations, and explore public demographic, economic, and health datasets with optional Pandas support.

Datamol Cheminformatics Toolkit

K-Dense-AI/claude-scientific-skills

Datamol wraps RDKit in a Pythonic API, delivering SMILES/SELFIES conversions, molecular sanitization, descriptors, fingerprints, 3D conformers, clustering, and cloud-friendly I/O for drug discovery workflows while keeping native rdkit.Chem.Mol compatibility.

Molecular ML Toolkit

K-Dense-AI/claude-scientific-skills

DeepChem is a Python library for molecular machine learning, bundling data loaders, featurizers, splitters, and models so researchers can rapidly predict molecular properties, benchmark on MoleculeNet, or build drug discovery and materials pipelines.

DeepTools NGS Analysis

K-Dense-AI/claude-scientific-skills

DeepTools is a Python toolkit for NGS QC, normalization, sample comparison, and visualization, covering BAM-to-bigWig conversion, fingerprint/correlation checks, and publication-ready heatmaps/profiles for ChIP-seq, RNA-seq, and ATAC-seq workflows.

DNAnexus Cloud Integration

dnanexus-integration

K-Dense-AI/claude-scientific-skills

Integrate with the DNAnexus cloud genomics platform to build, configure, and run bioinformatics apps, manage FASTQ/BAM/VCF datasets, orchestrate workflows, and script everything through the dxpy Python SDK for automated pipelines.

EDGAR Data Extractor

K-Dense-AI/claude-scientific-skills

Python library for accessing SEC EDGAR filings, extracting XBRL statements, insider trading, and institutional holdings data to power financial analysis, screening, or structured data workflows across 10-K/10-Q/8-K/DEF-14A filings.

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