Python

A comprehensive documentation skill for scvi-tools, a Python framework for probabilistic deep generative models in single-cell genomics. It provides guidance on models for RNA-seq, ATAC-seq, multimodal data integration, spatial transcriptomics, and specialized modalities like methylation and cytometry analysis.

A comprehensive reference skill for scikit-bio, a Python bioinformatics library. Provides documentation and code examples for biological sequence manipulation, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination analysis (PCoA, CCA), statistical tests (PERMANOVA, ANOSIM), and microbiome data processing with FASTA/BIOM file format support.

This skill provides a comprehensive toolkit for analyzing single-cell RNA-seq data using the scanpy library. It enables quality control, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, marker gene identification, cell type annotation, and publication-quality visualizations.

RDKit is a comprehensive cheminformatics skill that guides users through molecular analysis tasks including reading/writing chemical structures (SMILES, SDF), calculating molecular descriptors (LogP, TPSA, molecular weight), generating fingerprints for similarity searching, and performing substructure matching. It includes ready-to-use Python scripts for drug-likeness screening, similarity searches, and functional group filtering.

A comprehensive reference skill for QuTiP (Quantum Toolbox in Python), providing documentation for simulating open quantum systems, master equations, and quantum optics. Includes detailed guides for time evolution solvers, visualization tools, and advanced features like Floquet theory and HEOM methods.

This skill provides extensive guidance for working with IBM's Qiskit quantum computing framework. It covers building quantum circuits, running simulations, executing on real IBM Quantum hardware, and implementing quantum algorithms like VQE, QAOA, and Grover's search. The skill includes reference documentation for setup, primitives, transpilation, visualization, and various quantum applications in chemistry, optimization, and machine learning.

Pysam is a documentation skill for genomic data analysis using Python. It provides comprehensive reference guides for reading and writing sequencing alignment files (SAM/BAM/CRAM), genetic variant files (VCF/BCF), and sequence files (FASTA/FASTQ), along with practical code examples for bioinformatics workflows like coverage analysis and variant filtering.

PyLabRobot is a vendor-agnostic laboratory automation skill that helps you control liquid handling robots (Hamilton, Opentrons, Tecan), plate readers, pumps, heater shakers, and other lab equipment through a unified Python interface. It includes simulation capabilities for testing protocols without physical hardware.

A comprehensive reference skill for the Polars DataFrame library, providing documentation on data operations, pandas migration patterns, I/O operations, and performance best practices. Designed for users working with in-memory data processing tasks.

This skill provides comprehensive guidance for using Plotly, a Python library for creating interactive, publication-quality data visualizations. It covers 40+ chart types including scatter plots, bar charts, 3D surfaces, and geographic maps, along with styling, export options, and Dash integration for web applications.

Modal is a documentation skill that guides users in running Python code on Modal's serverless cloud platform. It covers GPU-accelerated computing, autoscaling, persistent storage with Volumes, scheduled jobs, and web endpoints for ML workloads and batch processing.

This skill helps chemists and drug discovery researchers filter and prioritize compound libraries using established medicinal chemistry rules like Lipinski's Rule of Five, PAINS filters, and structural alerts. It can process molecules in batch with parallel processing and generate detailed filtering reports.

This skill provides expert guidance on using matplotlib for data visualization in Python. It covers both pyplot and object-oriented interfaces, includes comprehensive reference documentation for plot types, styling, and troubleshooting, plus ready-to-use template scripts for creating publication-quality figures.

This skill provides comprehensive guidance for using the matchms Python library for mass spectrometry data processing and analysis. It covers spectral similarity calculations, compound identification from spectral libraries, data filtering, and format conversion for metabolomics research workflows.

Histolab is a documentation skill for the histolab Python library used in digital pathology. It provides comprehensive guidance on processing whole slide images (WSI), including tissue detection, tile extraction strategies, preprocessing filters, and visualization techniques for preparing datasets for deep learning pipelines.

FlowIO is a documentation skill that teaches Claude how to help users work with Flow Cytometry Standard (FCS) files. It provides guidance on parsing FCS metadata, extracting event data as NumPy arrays, creating new FCS files, and handling multi-dataset files for scientific flow cytometry data processing.

A comprehensive documentation skill for Dask, a Python library for parallel and distributed computing. It provides detailed reference guides for working with larger-than-memory datasets using DataFrames, Arrays, Bags, and Futures, along with scheduler selection and best practices for performance optimization.

COBRApy is a documentation skill for systems biology and metabolic engineering analysis. It provides comprehensive guidance on using the COBRApy Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, including flux balance analysis, gene knockouts, flux sampling, and SBML model handling.

This skill provides comprehensive documentation and code examples for Google's Cirq quantum computing framework. It covers quantum circuit design, simulation, noise modeling, hardware integration with multiple providers (Google, IonQ, Azure, AQT, Pasqal), and experiment design patterns like VQE and QAOA.

This skill provides comprehensive guidance for programmatically accessing the CZ CELLxGENE Census, a collection of 61+ million single-cell genomics data. It covers querying expression data by cell type, tissue, or disease, integrating with PyTorch for machine learning, and using scanpy for analysis workflows.

This skill provides comprehensive documentation and reference material for working with AnnData, a Python package for handling annotated data matrices used in single-cell genomics. It covers creating, reading, writing, and manipulating AnnData objects, along with best practices for memory management and integration with the scverse ecosystem (Scanpy, Muon, PyTorch).

This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.

Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.

Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.

Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.

Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.

Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.