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Scalable Regulatory Network Inference

K-Dense-AI/claude-scientific-skills

Infers gene regulatory networks from bulk or single-cell expression data via GRNBoost2/GENIE3 with distributed computing support, ideal for transcriptomics workflows seeking TF-target relationships at scale.

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.

BRENDA Enzyme Explorer

brenda-database

K-Dense-AI/claude-scientific-skills

Access the BRENDA SOAP API to retrieve enzyme kinetic parameters, reaction equations, organism-specific data, and environmental preferences, enabling biochemical research, metabolic pathway reconstruction, and enzyme engineering workflows.

Clinical Report Writing

clinical-reports

K-Dense-AI/claude-scientific-skills

Draft case reports, diagnostic summaries, trial documents, and patient notes with templates and compliance checks for HIPAA, FDA, and ICH-GCP, including schematics generation via scientific-schematics to visualize timelines, algorithms, or CONSORT flows.

ClinVar Variant Explorer

clinvar-database

K-Dense-AI/claude-scientific-skills

Query NCBI ClinVar for variant clinical significance, mixing gene/condition searches, API/FTP downloads, and VCF annotations to support genomic medicine interpretation workflows.

Distributed Dask Workflows

K-Dense-AI/claude-scientific-skills

Dask enables larger-than-memory pandas/NumPy workflows through parallel, distributed execution across dataframes, arrays, bags, and futures, making it ideal for scaling ETL, analytics, or custom computations across cores or clusters.

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.

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.

Denario Research Pipeline

K-Dense-AI/claude-scientific-skills

Denario orchestrates a multi-agent AI to automate research workflows, covering idea generation, methodology development, computational experiments, and LaTeX publication output.

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