About Deep-TEIRI

About

Deep-TEIRI is a pipeline to identify TE-initiated transcripts by integrating DNA sequence and RNA-seq coverage information with a deep-learning model.

The upstream repository includes:

• Pipeline scripts: https://github.com/yunzhang1998/Deep-TEIRI/tree/main/script

• Trained model files: https://github.com/yunzhang1998/Deep-TEIRI/tree/main/Model

Guides

• Installation

• Usage

• Example

License

See upstream repository for license details.

Citation

If you use TEIRI in your research, please cite:

• Yun Zhang, Jianqi She, Xueyan Hu, Yueqi Jin, Jiaming Zhao, Songyan Hou, Changyu Tao, Minghao Du, Ence Yang. Transposable elements drive species-specific and tissue-specific transcriptomes in human development. Genome Biology, 2025, 26:379, https://doi.org/10.1186/s13059-025-03855-5