mogam-ai/DuET-dataset

DuET TE measurements of 64 human cell types & benchmark datasets for TE and MRL prediction task

This dataset comprises TE datasets for 64 cell types and benchmark datasets for TE and MRL prediction task.

How to setup

First, clone the main repository to your work directory:

$ git clone https://github.com/mogam-ai/DuET.git
$ cd DuET

Then, download the dataset repository into DuET/datasets subdirectory.

# Needs huggingface-cli (pip install huggingface-cli)
$ huggingface-cli login
$ mkdir Duet/datasets
$ hf download mogam-ai/DuET-dataset --repo-type dataset --local-dir Duet/datasets

Dataset Details

Dataset Contents

• —64_celltypes_te: This directory contains transcript TEs for 64 human cell types.
• —mrl_benchmark: This directory contains eight benchmark MRL datasets created by Sample *et al.*
• —te_benchmark: This directory contains three benchmark TE datasets created by Cao *et al.*

Each directory also contains sequence feature dataset(s) for all transcripts.<br> For mrl_benchmark, sequence features were split into separate files due to file size.

Further information can be found at TBD.

Dataset Structure

*64_celltypes_te/\_TE.tsv**

• —txID: str, unique Ensembl transcript ID (GENCODE v47)
• —utr5: str, full length 5' UTR
• —cds: str, full length CDS
• —te: float, measured TE value

Train/test split were conducted at runtime (10-fold cross validation).

*mrl_benchmark/\.tsv**

• —txID: str, unique Ensembl transcript ID (GENCODE v47)
• —utr5: str, 50bp 5' UTR
• —te: float, measured MRL value provided by Sample et al.
• —readcount: int, sequenced read count (MPRA)

As in original paper, 20,000 sequences with the highest read counts for each dataset were selected as test set.

*te_benchmark/\.tsv**

• —txID: str, unique Ensembl transcript ID (GENCODE v17)
• —utr5: str, full length 5' UTR
• —cds: str, full length CDS
• —te: float, TE value provided by Cao et al.

Train/test split were conducted at runtime (10-fold cross validation).

sequence feature files<br> For detailed information, see TBD.

Citation

TBA

BibTeX:

TBA

APA:

TBA