Region2Vec ChIP-atlas hg38

Model Details

Model Description

This is a region2vec model trained on the hg38 ChIP-atlas ATAC-seq data

Developed by: Nathan LeRoy
Model type: Region2Vec
Language(s) (NLP): hg38

Model Sources [optional]

Repository: https://github.com/databio/geniml
Paper [optional]: https://academic.oup.com/bioinformatics/article/37/23/4299/6307720

Uses

This model can be used to generate embeddings of genomic regions or region sets. Once embeddings are obtained, they can be directly used for clustering, classification, or search and retrieval tasks. It is limited to hg38. It is not recommended to use this model for data outside ATAC-seq.

How to Get Started with the Model

You can download and start encoding new genomic region data using the following code:

from gitk.region2vec import Region2VecExModel

model = Region2VecExModel("databio/r2v-ChIP-atlas")
embeddings = model.encode("path/to/file.bed")

print(embeddings.shape)

[More Information Needed]

Training Details

Training Data

TODO