{"id":13752553,"url":"https://github.com/genentech/gReLU","last_synced_at":"2025-05-09T20:34:07.867Z","repository":{"id":241896837,"uuid":"788591787","full_name":"Genentech/gReLU","owner":"Genentech","description":"gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.","archived":false,"fork":false,"pushed_at":"2025-03-31T18:34:15.000Z","size":47236,"stargazers_count":256,"open_issues_count":28,"forks_count":30,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-04-12T04:45:18.713Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://genentech.github.io/gReLU/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-04-18T18:01:46.000Z","updated_at":"2025-04-02T14:35:03.000Z","dependencies_parsed_at":"2024-05-30T16:02:26.164Z","dependency_job_id":"9eee8073-cb71-4089-8130-86c22423a53f","html_url":"https://github.com/Genentech/gReLU","commit_stats":null,"previous_names":["genentech/grelu"],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FgReLU","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FgReLU/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FgReLU/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2FgReLU/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/gReLU/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253321671,"owners_count":21890445,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-03T09:01:07.479Z","updated_at":"2025-05-09T20:34:02.805Z","avatar_url":"https://github.com/Genentech.png","language":"Python","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"# gReLU\n\ngReLU 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/).\n\n![Flowchart](media/flowchart.jpg)\n\n## Installation\n\nTo install from source:\n\n```shell\ngit clone https://github.com/Genentech/gReLU.git\ncd gReLU\npip install .\n```\n\nTo install using pip:\n\n```shell\npip install gReLU\n```\n\n## Contributing\n\nThis project uses [pre-commit](https://pre-commit.com/). Please make sure to install it before making any changes:\n\n```shell\npip install pre-commit\ncd gReLU\npre-commit install\n```\n\nIt is a good idea to update the hooks to the latest version:\n\n```shell\npre-commit autoupdate\n```\n\n## Additional requirements\n\nIf 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`.\n\nIf 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`.\n\nUCSC utilities can be installed from `http://hgdownload.cse.ucsc.edu/admin/exe/`, for example using the following commands:\n\n```shell\nrsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/bin/\nrsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/genePredToBed /usr/bin/\nrsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/genePredToGtf /usr/bin/\nrsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedToGenePred /usr/bin/\nrsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/gtfToGenePred /usr/bin/\nrsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/gff3ToGenePred /usr/bin/\n```\n\nor via bioconda:\n\n```shell\nconda install -y \\\nbioconda::ucsc-bedgraphtobigwig \\\nbioconda::ucsc-genepredtobed    \\\nbioconda::ucsc-genepredtogtf    \\\nbioconda::ucsc-bedtogenepred    \\\nbioconda::ucsc-gtftogenepred    \\\nbioconda::ucsc-gff3togenepred\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2FgReLU","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2FgReLU","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2FgReLU/lists"}