Skill UI

Manage Zotero reference libraries programmatically with the pyzotero Python client and Zotero Web API v3. Retrieve, create, update and delete items, collections, tags and attachments; search libraries and export BibTeX or CSL-JSON citations for research automation workflows.

Qiskit is a Python framework for building, simulating, and executing quantum circuits. It supports local simulation, noisy simulation, and IBM Quantum hardware execution. Users can utilize V2 primitives like Sampler and Estimator for variational algorithms and quantum machine learning tasks.

Python cheminformatics toolkit for fine-grained molecular control: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D coordinate generation, similarity, reactions, and visualization.

Scanpy is a scalable Python toolkit for single-cell RNA-seq analysis, covering quality control, normalization, dimensionality reduction, clustering, and visualization. It supports converting R formats to h5ad and includes ready-to-run CLI scripts for end-to-end workflows, making it ideal for exploratory scRNA-seq analysis and publication-quality plotting.

Python toolkit for biological data: sequence manipulation, pairwise and multiple alignment, phylogenetic trees, alpha/beta diversity and UniFrac metrics, ordination (PCoA), PERMANOVA, and FASTA/Newick/BIOM I/O for microbiome analysis.

Comprehensive guidance for machine learning in Python using scikit-learn. Covers classification, regression, clustering, preprocessing, model evaluation, and pipelines for building production-ready ML workflows.

scVelo is a Python package for RNA velocity analysis in single-cell RNA-seq data. It estimates cell state transitions from unspliced/spliced mRNA dynamics, infers trajectory directions, computes latent time, and identifies driver genes to reveal cell fate decisions.

scvi-tools is a comprehensive Python framework for probabilistic deep generative models in single-cell genomics. Built on PyTorch and PyTorch Lightning, it enables batch correction, transfer learning, differential expression analysis with uncertainty, and multi-modal data integration. Best for advanced modeling of single-cell RNA-seq, ATAC-seq, CITE-seq, spatial transcriptomics, and specialized modalities like methylation and cytometry.

Seaborn is a Python visualization library built on matplotlib for creating statistical graphics. It integrates with pandas for dataset-oriented plotting, offering publication-quality defaults for distributions, relationships, and categorical comparisons. Ideal for exploratory data analysis, multivariate analysis, and complex multi-panel figures. Supports various plot types like box plots, violin plots, and heatmaps.

This skill covers using the SHAP library to explain and audit machine learning predictions. It guides users on selecting explainers, computing feature attributions, and validating results. It includes workflows for local and global visualizations, handling multi-output models, and ensuring model behavior descriptions are accurate without implying causality. Requires Python 3.12+ and specific SHAP versions.

A Python library for building and analyzing bounded process-based discrete-event simulations. Supports events, resources, interrupts, and monitoring for modeling queues, logistics, and service operations with reproducible output analysis and validation.

Production-ready reinforcement learning library with PPO, SAC, DQN, TD3, DDPG, A2C algorithms. Use for training RL agents, creating custom environments, implementing callbacks, and optimizing training workflows. Best for single-agent RL with Gymnasium environments. Requires Python 3.10+ and PyTorch >= 2.3.