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 pip install geniml

For ML dependencies (PyTorch, etc.):

uv pip install 'geniml[ml]'