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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.

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.

Scaling Pandas with Dask

K-Dense-AI/claude-scientific-skills

Dask is a Python library that scales pandas/NumPy workflows beyond RAM by parallelizing DataFrames, Arrays, Bags, and custom tasks across cores or clusters for ETL, log analysis, and distributed ML.

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 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.

Molecular ML Toolkit

K-Dense-AI/claude-scientific-skills

DeepChem is a Python library for molecular machine learning, providing featurizers, dataset loaders, splitters, and models spanning traditional ML to GNNs for property prediction, drug discovery, and materials design.

NGS Data Visualization

K-Dense-AI/claude-scientific-skills

deepTools is a Python command-line suite for NGS workflows, converting BAM files into normalized coverage, running QC (fingerprint, correlation, PCA), comparing samples, and rendering heatmaps or profiles for ChIP-seq, RNA-seq, and ATAC-seq analyses.

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.

DiffDock Pose Predictor

K-Dense-AI/claude-scientific-skills

DiffDock uses diffusion-based deep learning to predict protein-ligand binding poses, confidence, and batch virtual screening workflows for structure-based drug design.

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.

DrugBank Database Insights

drugbank-database

K-Dense-AI/claude-scientific-skills

Provides programmatic access to DrugBank drug and target data, covering downloads, queries, interaction networks, targets/pathways, and chemical similarity analyses for pharmacology research and safety reviews.

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