geniml
Geniml: Genomic Interval Machine Learning
Overview
Geniml is a Python package for building machine learning models on genomic interval data from BED files. It provides unsupervised methods for learning embeddings of genomic regions, single cells, and metadata labels, enabling similarity searches, clustering, and downstream ML tasks.
Installation
Install geniml using uv:
uv uv pip install geniml
For ML dependencies (PyTorch, etc.):
uv uv pip install 'geniml[ml]'
More from wu-yc/labclaw
tooluniverse-chemical-safety
Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions. Performs predictive toxicology (AMES, DILI, LD50, carcinogenicity), organ/system toxicity profiling, chemical-gene-disease relationship mapping, regulatory safety extraction, and environmental hazard assessment. Use when asked about chemical toxicity, drug safety profiling, ADMET properties, environmental health risks, chemical hazard assessment, or toxicogenomic analysis.
20rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.
19tooluniverse-protein-therapeutic-design
Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMPNN for sequence design, ESMFold/AlphaFold2 for validation. Use when asked to design protein binders, therapeutic proteins, or engineer protein function.
19tooluniverse-drug-repurposing
Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies. Searches existing drugs for new therapeutic indications by analyzing targets, bioactivity, safety profiles, and literature evidence. Use when exploring drug repurposing opportunities, finding new indications for approved drugs, or when users mention drug repositioning, off-label uses, or therapeutic alternatives.
19tooluniverse-drug-research
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections. Covers identity, chemistry, pharmacology, targets, clinical trials, safety, pharmacogenomics, and ADMET properties. Use when users ask about drugs, medications, therapeutics, or need drug profiling, safety assessment, or clinical development research.
19tooluniverse-pharmacovigilance
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug safety, adverse events, post-market surveillance, or risk-benefit assessment.
19