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Biopython Molecular Toolkit

K-Dense-AI/claude-scientific-skills

Biopython provides Python APIs for sequence manipulation, database access, BLAST automation, structural bioinformatics, and phylogenetics, making it ideal for scripting custom pipelines and batch processing in computational molecular biology workflows.

BioServices Cross-DB API

K-Dense-AI/claude-scientific-skills

BioServices provides Python wrappers for 40+ bioinformatics services, allowing cross-database queries, identifier mapping, pathway exploration, and sequence or compound research within consistent workflows.

Cirq Quantum Toolkit

K-Dense-AI/claude-scientific-skills

Cirq is Google Quantum AI’s Python framework for building, simulating, and deploying noise-aware quantum circuits on both simulators and real hardware, complete with experiment templates, transformation utilities, and hardware-specific toolkits.

Academic Citation Manager

citation-management

K-Dense-AI/claude-scientific-skills

Streamlines citation discovery via Google Scholar and PubMed, extracts complete metadata, validates references, and generates formatted BibTeX for accurate academic manuscripts or theses.

COBRApy Metabolic Analysis

K-Dense-AI/claude-scientific-skills

COBRApy is a Python library for constraint-based reconstruction and analysis of genome-scale metabolic models, letting you load SBML/JSON/YAML models, perform FBA/FVA/sampling, and study gene or reaction knockouts for systems biology and metabolic engineering.

COSMIC Mutation Access

cosmic-database

K-Dense-AI/claude-scientific-skills

Programmatic access to the COSMIC cancer mutation database for downloading mutations, Cancer Gene Census, mutational signatures, fusions, copy number, expression, and resistance data to fuel oncology research or bioinformatics pipelines after authentication.

Datamol Cheminformatics Helper

K-Dense-AI/claude-scientific-skills

Datamol wraps RDKit with Pythonic APIs tailored for drug discovery, offering SMILES/SELFIES/InChI parsing, standardization, descriptor and fingerprint calculation, clustering, 3D conformer workflows, and parallel/cloud-aware batch I/O while returning native rdkit.Chem.Mol objects.

DNAnexus Cloud Genomics

dnanexus-integration

K-Dense-AI/claude-scientific-skills

Integrate with the DNAnexus cloud genomics platform to build apps/applets, manage FASTQ/BAM/VCF data, run workflows, and script automations via dxpy for biomedical 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.

ENA Sequence Access

K-Dense-AI/claude-scientific-skills

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

Scientific Data Exploration

exploratory-data-analysis

K-Dense-AI/claude-scientific-skills

Automates detection and deep exploratory analysis across 200+ scientific data formats, assessing quality, extracting metadata, and recommending visualizations while generating markdown reports that guide downstream workflows and highlight structure and distributions.

GEO Data Retriever

K-Dense-AI/claude-scientific-skills

Connect to NCBI's GEO repository, search series/samples/platforms via Entrez queries, fetch profiles, and download raw/processed matrices using GEOparse for transcriptomics and expression analysis workflows.

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