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GeoPandas Spatial Toolkit

K-Dense-AI/claude-scientific-skills

GeoPandas extends pandas for geospatial vector data, enabling reading/writing shapefiles, GeoJSON, GeoPackage and PostGIS, performing CRS management, spatial joins, overlays, buffering, area/distance calculations, and producing static or interactive choropleth maps.

Genomic Interval Toolkit

K-Dense-AI/claude-scientific-skills

High-performance Rust toolkit with Python bindings for genomic interval analysis, covering overlap detection, coverage track generation, ML tokenization, reference sequence handling, fragment processing, and scoring workflows for sequencing datasets.

KEGG REST Toolkit

K-Dense-AI/claude-scientific-skills

Direct Python helpers for KEGG's REST API, covering database metadata, listing, search, retrieval, ID conversion, linkage, and drug interactions to power pathway and gene analysis.

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.

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.

Medical Imaging DICOM Toolkit

K-Dense-AI/claude-scientific-skills

Pydicom is a Python toolkit for reading, writing, and manipulating DICOM medical imaging files, helping teams extract pixel data, manage metadata, anonymize records, convert to standard formats, and integrate with PACS workflows in healthcare research and radiology applications.

Materials Structure Toolkit

K-Dense-AI/claude-scientific-skills

A Python materials science library for constructing, analyzing, and converting crystal structures, computing phase diagrams and electronic properties, and integrating with the Materials Project API for high-throughput workflows.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

Advanced Molecular Control

K-Dense-AI/claude-scientific-skills

RDKit delivers a Python-based cheminformatics toolkit for parsing SMILES/SDF, computing descriptors, generating 2D/3D coordinates, fingerprinting, searching substructures, managing reactions, and visualizing molecules, ideal for drug discovery and computational chemistry workflows.

Scanpy Single-Cell Workflow

K-Dense-AI/claude-scientific-skills

Scanpy is a scalable Python toolkit for single-cell RNA-seq analyses, covering QC, normalization, dimensionality reduction, clustering, marker discovery, annotation, and publication-ready visualization across h5ad/10X/CSV datasets.

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