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https://github.com/genentech/gReLU
gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
https://github.com/genentech/gReLU
Last synced: about 2 months ago
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gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
- Host: GitHub
- URL: https://github.com/genentech/gReLU
- Owner: Genentech
- License: mit
- Created: 2024-04-18T18:01:46.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2024-11-04T22:29:11.000Z (2 months ago)
- Last Synced: 2024-11-04T22:33:07.751Z (2 months ago)
- Language: Python
- Homepage: https://genentech.github.io/gReLU/
- Size: 36.3 MB
- Stars: 223
- Watchers: 9
- Forks: 23
- Open Issues: 27
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Authors: AUTHORS.md
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README
# gReLU
gReLU is a Python library to train, interpret, and apply deep learning models to DNA sequences. Code documentation is available [here](https://genentech.github.io/gReLU/).
## Installation
To install from source:
```shell
git clone https://github.com/Genentech/gReLU.git
cd gReLU
pip install .
```
To install using pip:
```shell
pip install gReLU
```
## Contributing
This project uses [pre-commit](https://pre-commit.com/). Please make sure to install it before making any changes:
```shell
pip install pre-commit
cd gReLU
pre-commit install
```
It is a good idea to update the hooks to the latest version:
```shell
pre-commit autoupdate
```
## Additional requirements
If you want to use genome annotation features through the function `grelu.io.genome.read_gtf`, you will need to install the following UCSC utilities: `genePredToBed`, `genePredToGtf`, `bedToGenePred`, `gtfToGenePred`, `gff3ToGenePred`.
If you want to create bigWig files through the function `grelu.data.preprocess.make_insertion_bigwig`, you will need to install the following UCSC utilities: `bedGraphToBigWig`.
UCSC utilities can be installed from `http://hgdownload.cse.ucsc.edu/admin/exe/`, for example using the following commands:
```shell
rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/bin/
rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/genePredToBed /usr/bin/
rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/genePredToGtf /usr/bin/
rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedToGenePred /usr/bin/
rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/gtfToGenePred /usr/bin/
rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/gff3ToGenePred /usr/bin/
```
or via bioconda:
```shell
conda install -y \
bioconda::ucsc-bedgraphtobigwig \
bioconda::ucsc-genepredtobed \
bioconda::ucsc-genepredtogtf \
bioconda::ucsc-bedtogenepred \
bioconda::ucsc-gtftogenepred \
bioconda::ucsc-gff3togenepred
```