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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.

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.

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.

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.

Ensembl Genome API

ensembl-database

K-Dense-AI/claude-scientific-skills

Query Ensembl’s RESTful API to access gene annotations, sequences, variants, orthologs, and assembly mappings across 250+ species, enabling integration into genomic research pipelines.

Phylogenetic Tree Toolkit

K-Dense-AI/claude-scientific-skills

A toolkit for phylogenetic tree manipulation, event detection, NCBI taxonomy integration, and publication-quality visualization, streamlining phylogenomics workflows and gene family analysis.

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.

FDA Regulatory Data Access

K-Dense-AI/claude-scientific-skills

Provides Python access to openFDA endpoints for drugs, devices, foods, veterinary products, and substances, enabling regulatory analysis, safety monitoring, recalls tracking, and pharmacovigilance research.

FlowIO FCS Handler

K-Dense-AI/claude-scientific-skills

FlowIO reads and writes Flow Cytometry Standard (FCS) files, exposing metadata, channels, and NumPy event arrays while allowing CSV/DataFrame conversion, making it ideal for cytometry pipelines and backend preprocessing services.

FRED Economic Data API

fred-economic-data

K-Dense-AI/claude-scientific-skills

Access over 800,000 economic time series from FRED's API, covering GDP, employment, inflation, interest rates, regional metrics, and more; ideal for macroeconomic analysis, financial research, policymaking, and forecasting workflows.

NCBI Gene Explorer

K-Dense-AI/claude-scientific-skills

Access NCBI Gene data via E-utilities or Datasets API to look up genes by symbol or ID, retrieve RefSeqs, GO terms, chromosomal locations, phenotypes, and run batch workflows for annotation pipelines.

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