Atacformer is a general-purpose transformer-based foundation model for genomic interval data, specifically designed for ATAC-seq data. It is part of the Geniml toolkit, which provides a suite of tools for genomic interval machine learning. Trained on a large corpus of ATAC-seq data, Atacformer can be fine-tuned for various downstream tasks such as classification, regression, and sequence generation.
All pre-trained models are available on the Hugging Face Hub, and you can easily load them using the geniml
package:
from geniml.atacformer import AtacformerForCellClustering
model = AtacformerForCellClustering.from_pretrained("databio/atacformer-base-hg38")