Utilities for training DL models using DNA sequence and chromatin inputs
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Project description
seqchromloader
seqchromloader aims to provide versatile and ready-to-use writer/loader for applying deep learning to bioinformatics study.
Plan to support dataset formats including:
- webdataset (done)
- tfrecord (x)
Training framework support:
- pytorch dataloader (done)
- pytorch-lightning datamodule (done)
- NVIDIA-DALI (x)
Installation
conda (suggested):
mamba install -c bioconda -c conda-forge seqchromloader
or
conda install -c bioconda -c conda-forge seqchromloader
pip
pip install seqchromloader
Usage
For detailed usage, please refer to documentation
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