Find the best CLAUDE.md, AGENTS.md and Claude skills

tondevrelSkill

mne

tondevrel/scientific-agent-skills/skills/mne/SKILL.md

Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data including EEG, MEG, sEEG, and ECoG.

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networkx

tondevrel/scientific-agent-skills/skills/networkx/SKILL.md

Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Supports various graph types (Directed, Undirected, Multigraphs) and features a vast library of standard graph algorithms. Use for network analysis, graph theory, social network analysis, biological networks, infrastructure networks, path finding, centrality measures, community detection, graph algorithms, shortest paths, PageRank, connectivity analysis, and routing optimization.

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numba

tondevrel/scientific-agent-skills/skills/numba/SKILL.md

A Just-In-Time (JIT) compiler for Python that translates a subset of Python and NumPy code into fast machine code. Developed by Anaconda, Inc. Highly effective for accelerating loops, custom mathematical functions, and complex numerical algorithms. Use for @njit, @vectorize, prange, cuda.jit, numba.typed, JIT compilation, parallel loops, GPU acceleration with CUDA, Monte Carlo simulations, numerical algorithms, and high-performance Python computing.

tondevrelSkill

numpy-low-level

tondevrel/scientific-agent-skills/skills/numpy-low-level/SKILL.md

Advanced sub-skill for NumPy focused on internal memory management, stride manipulation, structured arrays, and interfacing with C/Cython. Covers zero-copy operations and SIMD vectorization principles.

tondevrelSkill

numpy

tondevrel/scientific-agent-skills/skills/numpy/SKILL.md

Comprehensive guide for NumPy - the fundamental package for scientific computing in Python. Use for array operations, linear algebra, random number generation, Fourier transforms, mathematical functions, and high-performance numerical computing. Foundation for SciPy, pandas, scikit-learn, and all scientific Python.

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openbabel

tondevrel/scientific-agent-skills/skills/openbabel/SKILL.md

A chemical toolbox designed to speak the many languages of chemical data. Supports over 110 formats and provides tools for conversion, 3D structure generation, molecular searching (SMARTS), and force field calculations. Use for chemical file format conversion (SDF, PDB, SMILES, CIF, Gaussian), 3D coordinate generation from 2D structures, substructure searching with SMARTS patterns, molecular docking preparation, force field minimizations (UFF, GAFF, MMFF94), molecular fingerprints and Tanimoto coefficients, and batch processing of chemical databases.

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opencv

tondevrel/scientific-agent-skills/skills/opencv/SKILL.md

Open Source Computer Vision Library (OpenCV) for real-time image processing, video analysis, object detection, face recognition, and camera calibration. Use when working with images, videos, cameras, edge detection, contours, feature detection, image transformations, object tracking, optical flow, or any computer vision task.

tondevrelSkill

ortools

tondevrel/scientific-agent-skills/skills/ortools/SKILL.md

Google Optimization Tools. An open-source software suite for optimization, specialized in vehicle routing, flows, integer and linear programming, and constraint programming. Features the world-class CP-SAT solver. Use for vehicle routing problems (VRP), scheduling, bin packing, knapsack problems, linear programming (LP), integer programming (MIP), network flows, constraint programming, combinatorial optimization, resource allocation, shift scheduling, job-shop scheduling, and discrete optimization problems.

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pandas-performance

tondevrel/scientific-agent-skills/skills/pandas-performance/SKILL.md

Advanced sub-skill for pandas focused on memory optimization, execution speed, and handling large-scale datasets (10M+ rows). Covers low-level dtypes, efficient indexing, and vectorization of complex logic.

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pennylane

tondevrel/scientific-agent-skills/skills/pennylane/SKILL.md

Cross-platform Python library for differentiable quantum computing. Integrated with machine learning libraries like PyTorch, TensorFlow, and JAX. Designed for quantum machine learning (QML), variational algorithms, and hardware-agnostic quantum programming. Use for Quantum Neural Networks (QNNs), Variational Quantum Algorithms (VQE, QAOA), hybrid classical-quantum machine learning, quantum chemistry calculations, benchmarking quantum algorithms, optimizing quantum control pulses, and investigating QML phenomena like Barren Plateaus.

tondevrelSkill

photutils

tondevrel/scientific-agent-skills/skills/photutils/SKILL.md

An Astropy coordinated package for detecting and performing photometry of astronomical sources. Provides tools for background estimation, source detection (DAOFIND, IRAF), aperture photometry, and PSF (Point Spread Function) fitting. Use when working with astronomical image analysis, star/galaxy detection, measuring brightness (photometry), background subtraction, PSF fitting, aperture photometry, centroiding, or isophotal analysis.

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plotly

tondevrel/scientific-agent-skills/skills/plotly/SKILL.md

A high-level interactive graphing library for Python. Ideal for web-based visualizations, 3D plots, and complex interactive dashboards. Built on plotly.js, it allows users to zoom, pan, and hover over data points in a browser-based environment. Use for interactive charts, web applications, Jupyter notebooks, 3D data visualization, geographic maps, financial charts, animations, time-series analysis, and building production-ready dashboards with Dash.

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polars

tondevrel/scientific-agent-skills/skills/polars/SKILL.md

Blazingly fast DataFrame library written in Rust. Features a multi-threaded query engine, lazy evaluation, and efficient memory usage via Apache Arrow. Designed for high-performance data processing on a single machine. Use for large datasets (1GB-100GB+), fast data transformations, Parquet/CSV processing, complex query pipelines, memory-efficient operations, and when speed is critical (10-100x faster than pandas).

Often used withusfiscaldata·deeptools·dnanexus-integration

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prody

tondevrel/scientific-agent-skills/skills/prody/SKILL.md

Protein Dynamics, Evolution, and Structure analysis. Specialized in Normal Mode Analysis (NMA) using Anisotropic (ANM) and Gaussian Network Models (GNM). Features tools for structural ensemble analysis, PCA, and co-evolutionary analysis (Evol). Use for protein flexibility prediction, collective motions, structural ensemble comparison, hinge region identification, binding site analysis, MD trajectory filtering, and evolutionary analysis.

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pydicom

tondevrel/scientific-agent-skills/skills/pydicom/SKILL.md

Python package for working with DICOM files. It allows you to read, modify, and write DICOM data in a Pythonic way. Essential for medical imaging processing, clinical data extraction, and AI in radiology.

Often used withusfiscaldata·deeptools·dnanexus-integration

tondevrelSkill

pymc

tondevrel/scientific-agent-skills/skills/pymc & numpyro/SKILL.MD

Probabilistic programming for Bayesian statistical modeling and inference. PyMC provides declarative model specification with MCMC (NUTS) and variational inference samplers; NumPyro offers JAX-accelerated equivalent for large-scale problems. Use when: quantifying uncertainty in parameter estimates, building hierarchical or mixed-effects models, Bayesian A/B testing or experimentation, posterior predictive checks, model comparison with WAIC or LOO-CV, scientific measurement with error propagation, any analysis requiring credible intervals, probability statements like P(effect > 0), or situations where understanding the full posterior distribution matters more than a single p-value. Also use when priors encode domain knowledge, sample sizes are small, or data is naturally nested.

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pyomo

tondevrel/scientific-agent-skills/skills/pyomo/SKILL.md

Python Optimization Modeling Objects. A high-level framework for formulating, solving, and analyzing optimization models. Supports Linear Programming (LP), Mixed-Integer Linear Programming (MILP), and Non-Linear Programming (NLP). Part of the COIN-OR project. Use for mathematical optimization, linear programming, mixed-integer programming, non-linear programming, strategic planning, process engineering, energy systems, supply chain optimization, stochastic programming, and solver integration with IPOPT, SCIP, Gurobi, CPLEX, or GLPK.

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pyproj

tondevrel/scientific-agent-skills/skills/pyproj/SKILL.md

Python interface to PROJ (cartographic projections and coordinate transformations library). Handles transformations between different Coordinate Reference Systems (CRS) and performs geodetic calculations (distance, area on ellipsoids). Use for coordinate transformations, CRS conversions, geodetic calculations, UTM projections, GPS coordinate conversions, ellipsoidal distance calculations, and spatial reference system operations.

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pysam

tondevrel/scientific-agent-skills/skills/pysam/SKILL.md

Python module for reading, manipulating and writing genomic alignment formats (SAM/BAM/CRAM) and variant files (VCF/BCF). Wrapper for htslib.

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pyscf

tondevrel/scientific-agent-skills/skills/pyscf/SKILL.md

Comprehensive guide for PySCF - Python-based Simulations of Chemistry Framework. Use for ab initio quantum chemistry calculations including Hartree-Fock, DFT, MP2, CCSD, geometry optimization, excited states, and molecular properties. Industry-standard library for electronic structure calculations.