Skill UI

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.

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.

Manage microscopy data with the OMERO Python API: access projects/datasets/images, retrieve and analyze pixel data, handle ROIs and annotations, store results in tables, and automate batch workflows for high-content screening.

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.

Hardware-agnostic quantum ML framework enabling gradient-based training of quantum circuits, hybrid quantum-classical models, and seamless integration with PyTorch/JAX/TensorFlow alongside device portability across IBM/Google/Rigetti/IonQ.

A comprehensive toolkit for reconstructing and analyzing the evolutionary history of biological sequences (genes, proteins, genomes). The standard workflow includes multiple sequence alignment using MAFFT, robust maximum likelihood tree inference with IQ-TREE 2 and FastTree, and advanced visualization/manipulation using ETE3. This skill is essential for studies in viral phylodynamics, microbial genomics, protein family evolution, and molecular clock dating.

polars-bio accelerates genomic interval math and bioinformatics I/O by combining Polars, Arrow, and DataFusion to handle BED/VCF/BAM/GFF/FASTA streams, SQL queries, and cloud storage with overlap, coverage, and nearest APIs plus streaming fallbacks.

Design research posters with HTML/CSS templates that export to PDF or PPTX when PowerPoint format is explicitly requested, integrating responsive layouts and AI-generated visuals for quick preview and iteration.

This skill provides complete, programmatic integration with the protocols.io API v3, enabling advanced management of scientific protocols. Use it for the entire protocol lifecycle, including discovery by DOI or keywords, creating new protocols, managing steps and materials, coordinating collaborative development, organizing workspaces, and tracking experiments. It covers authentication, file handling, and discussion management, making it ideal for automated lab workflows and scientific documentation systems.

PufferLib is a high-performance library designed for advanced reinforcement learning simulations and training. It excels in parallel environment simulation, offering optimized vectorization and native support for multi-agent systems. Utilizing algorithms like PuffeRL (optimized PPO+LSTM), it achieves millions of steps per second, significantly accelerating research and deployment across single-agent and multi-agent environments.

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

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.