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Mass Spectra Matching

K-Dense-AI/claude-scientific-skills

Matchms is an open-source Python toolkit for metabolomics mass spectrometry workflows: import and export diverse spectra, standardize metadata, filter peaks, score spectral similarity (cosine/modified cosine), and build pipelines to identify unknown compounds from libraries.

MATLAB Octave Toolkit

K-Dense-AI/claude-scientific-skills

MATLAB Octave Toolkit provides guidance for MATLAB and GNU Octave scripting, covering matrix math, visualization, data I/O, control flow, statistics, differential equations, and signal processing workflows.

Matplotlib Visualization Guide

K-Dense-AI/claude-scientific-skills

Matplotlib is Python’s foundational plotting toolkit for creating static, animated, and interactive charts with fine-grained control via both pyplot and object-oriented APIs, making it ideal for scientific publications, notebooks, and GUI workflows.

Medchem Filtering Toolkit

K-Dense-AI/claude-scientific-skills

Medchem is a Python library for applying drug-likeness rules, structural alerts, and complexity metrics to triage compound libraries. Run rule sets, catalogs, and custom constraints with parallel filtering, aiding lead optimization and quality control workflows.

Network Analysis Toolkit

K-Dense-AI/claude-scientific-skills

Provides Python-based tools for building, analyzing, and visualizing graph or network data, covering creation, algorithms (shortest paths, centrality, communities), generation, I/O, and rendering for domains like social, biological, or transport systems.

Biosignal Processing Toolkit

K-Dense-AI/claude-scientific-skills

NeuroKit2 is a Python toolkit for processing ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals, making it easy to derive HRV, ERP, complexity, autonomic, and multimodal assessments for psychophysiology research and clinical integrations.

Neuropixels Recording Analysis

neuropixels-analysis

K-Dense-AI/claude-scientific-skills

Toolkit for Neuropixels neural recording analysis that loads SpikeGLX/Open Ephys/NWB data, preprocesses, corrects motion, runs Kilosort4/alternative sorters, computes quality metrics, curates units via Allen/IBL criteria, renders visualizations, and exports to Phy or NWB for publication-ready results.

Pathology Imaging Toolkit

K-Dense-AI/claude-scientific-skills

PathML is a Python toolkit for computational pathology, enabling whole-slide image loading, stain-aware preprocessing, spatial graph construction, and machine learning workflows on multiplexed immunofluorescence data.

PyHealth Clinical AI Toolkit

K-Dense-AI/claude-scientific-skills

PyHealth is a Python healthcare AI toolkit for building, training, evaluating, and deploying clinical prediction models using EHR, signal, imaging, and coding data while optimizing pipelines, calibration, and interpretability.

Materials Structure Toolkit

K-Dense-AI/claude-scientific-skills

Pymatgen is a Python toolkit for computational materials science that creates, manipulates, and analyzes crystal structures, converts among 100+ formats, computes phase diagrams, and accesses Materials Project data for high-throughput workflows.

Pymoo Multi Objective Optimizer

K-Dense-AI/claude-scientific-skills

Pymoo is a Python optimization toolkit focused on multi-objective engineering problems, providing algorithms like NSGA-II/III, MOEA/D, customizable operators, benchmarks, and visualization helpers for Pareto analysis and constrained search.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam provides Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, letting developers query regions, compute coverage, and orchestrate NGS pipelines.

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