Agent skills
Skills you can use with AI coding agents, indexed from public GitHub repositories.
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histolab
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
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zarr-python
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
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tooluniverse
Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.
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rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
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deepchem
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
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pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
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medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
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torchdrug
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.
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diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
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datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
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molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
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canvas-design
Create beautiful visual art in .png and .pdf documents using design philosophy. You should use this skill when the user asks to create a poster, piece of art, design, or other static piece. Create original visual designs, never copying existing artists' work to avoid copyright violations.
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Algorithmic Art Generation
Create algorithmic art using p5.js with seeded randomness, flow fields, and
particle systems. Use when you need to generate generative art, create
computational aesthetics, or build interactive artistic visualizations.
Automatically activates when discussing: "generative art", "algorithmic art",
"p5.js visualization", "computational aesthetics".
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webapp-testing
Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
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markdown-to-epub-converter
Convert markdown documents and chat summaries into formatted EPUB ebook files that can be read on any device or uploaded to Kindle.
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markdown-to-epub-converter
Convert markdown documents and chat summaries into formatted EPUB ebook files that can be read on any device or uploaded to Kindle.
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markdown-to-epub-converter
Convert markdown documents and chat summaries into formatted EPUB ebook files that can be read on any device or uploaded to Kindle.
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youtube-transcript
Download YouTube video transcripts when user provides a YouTube URL or asks to download/get/fetch a transcript from YouTube. Also use when user wants to transcribe or get captions/subtitles from a YouTube video.
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video-downloader
Downloads videos from YouTube and other platforms for offline viewing, editing, or archival. Handles various formats and quality options.
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image-enhancer
Improves the quality of images, especially screenshots, by enhancing resolution, sharpness, and clarity. Perfect for preparing images for presentations, documentation, or social media posts.
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benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
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omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
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labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
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dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
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