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.

When to Use This Skill

Use this skill for ML over genomic intervals: training or applying Region2Vec / scEmbed / BEDspace embeddings, building consensus universes for tokenization, clustering scATAC-seq cells from region tokens, or BEDshift null models and BBClient caching.

Does NOT Trigger