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Matchms Spectral Matching

K-Dense-AI/claude-scientific-skills

Matchms processes LC-MS/MS spectra with import/export tools, filtering, and multiple similarity scorers so you can identify metabolites, match libraries, and automate reproducible workflows.

Metabolomics Workbench API

metabolomics-workbench-database

K-Dense-AI/claude-scientific-skills

Query the NIH Metabolomics Workbench via REST API to fetch metabolites, RefMet nomenclature, mass-spec searches, and detailed study datasets for biomarker discovery and metabolomics research.

Molecular Featurization Hub

K-Dense-AI/claude-scientific-skills

Molfeat is a Python toolkit that converts SMILES/RDKit molecules into embeddings via 100+ calculators, transformers, and pretrained models for QSAR, screening, similarity search, and deep learning pipelines.

NeuroKit2 Biosignal Processing

K-Dense-AI/claude-scientific-skills

NeuroKit2 is a Python biosignal processing toolkit for ECG, EEG, EDA, RSP, EMG, and EOG data that automates cleaning, feature extraction, and HRV/complexity analysis for psychophysiology, clinical, and HCI studies.

Neuropixels Analysis Toolkit

neuropixels-analysis

K-Dense-AI/claude-scientific-skills

End-to-end Neuropixels recording analysis covering SpikeGLX/OpenEphys/NWB loading, preprocessing, motion correction, Kilosort4 sorting, quality metrics, Allen/IBL curation, and AI-assisted visualization for extracellular electrophysiology.

OpenAlex Research Explorer

openalex-database

K-Dense-AI/claude-scientific-skills

Use the OpenAlex client to query 240M+ scholarly works for literature searches, citation tracking, open access discovery, and bibliometric studies across papers, authors, and institutions.

Open Targets Explorer API

opentargets-database

K-Dense-AI/claude-scientific-skills

Provides GraphQL queries to the Open Targets Platform for target-disease associations, tractability, safety, drugs, and multi-omics evidence to guide therapeutic target identification, safety assessment, and repurposing research workflows.

PathML Computational Pathology Toolkit

K-Dense-AI/claude-scientific-skills

PathML is a Python toolkit for computational pathology workflows, loading 160+ slide formats, preprocessing H&E images, constructing spatial graphs, training HoVer-Net/HACTNet models, and analyzing multiplex imaging for ML-ready pathology data.

PDB Structure Explorer

K-Dense-AI/claude-scientific-skills

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

Scientific Peer Review Checklist

K-Dense-AI/claude-scientific-skills

Structured manuscript and grant review guidance that walks reviewers through methodology, statistics, reporting compliance, and constructive feedback for rigorous scientific evaluation across disciplines.

Plotly Interactive Charts

K-Dense-AI/claude-scientific-skills

Plotly is a Python graphing library for interactive, publication-quality visuals that bring hover, zoom, animation, and dashboard-ready exports to exploratory analysis and presentations.

PubMed Database Access

pubmed-database

K-Dense-AI/claude-scientific-skills

Direct REST/API access to PubMed for constructing complex Boolean or MeSH queries, filtering by publication attributes, and automating literature retrieval or citation management via NCBI’s E-utilities.

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