gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences. Code documentation is available here.
To install from source:
git clone https://github.com/Genentech/gReLU.git
cd gReLU
pip install .
This project uses pre-commit. Please make sure to install it before making any changes:
pip install pre-commit
cd gReLU
pre-commit install
It is a good idea to update the hooks to the latest version:
pre-commit autoupdate
If you want to use genome annotation features through the function grelu.io.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:
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:
conda install bioconda::ucsc-bedgraphtobigwig
conda install bioconda::ucsc-genepredtobed
conda install bioconda::ucsc-genepredtogtf
conda install bioconda::ucsc-bedtogenepred
conda install bioconda::ucsc-gtftogenepred
conda install bioconda::ucsc-gff3togenepred