AI & LLM

datacommons-client @jackspace

Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use...

datamol @jackspace

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug...

deepchem @jackspace

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks,...

deeptools @jackspace

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks),...

denario @jackspace

Multiagent AI system for scientific research assistance that automates research workflows from data analysis to...

diffdock @jackspace

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual...

esm @jackspace

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across...

etetoolkit @jackspace

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy,...

flowio @jackspace

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert...

geniml @jackspace

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for...

gget @jackspace

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases:...

gtars @jackspace

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic...

histolab @jackspace

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with...

hypogenic @jackspace

Automated hypothesis generation and testing using large language models. Use this skill when generating scientific...

lamindb @jackspace

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data...

markitdown @jackspace

Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown...

matchms @jackspace

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata...

matplotlib @jackspace

Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export...

medchem @jackspace

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts,...

molfeat @jackspace

Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert...

networkx @jackspace

Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when...

neurokit2 @jackspace

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG,...

paper-2-web @jackspace

This skill should be used when converting academic papers into promotional and presentation formats including...

pathml @jackspace

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this...