{"id":18598214,"url":"https://github.com/cmdoret/sequence_loopability","last_synced_at":"2025-05-16T14:11:07.443Z","repository":{"id":93341572,"uuid":"352033748","full_name":"cmdoret/sequence_loopability","owner":"cmdoret","description":"Investigating sequence features underlying chromatin loops","archived":false,"fork":false,"pushed_at":"2021-06-03T13:58:42.000Z","size":7817,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-17T23:47:34.978Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cmdoret.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-03-27T09:37:56.000Z","updated_at":"2022-06-10T16:29:05.000Z","dependencies_parsed_at":"2023-03-07T18:00:41.288Z","dependency_job_id":null,"html_url":"https://github.com/cmdoret/sequence_loopability","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fsequence_loopability","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fsequence_loopability/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fsequence_loopability/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdoret%2Fsequence_loopability/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdoret","download_url":"https://codeload.github.com/cmdoret/sequence_loopability/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254544159,"owners_count":22088808,"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":"2024-11-07T01:31:38.762Z","updated_at":"2025-05-16T14:11:07.426Z","avatar_url":"https://github.com/cmdoret.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# sequence_loopability\nInvestigating the sequence features underlying chromatin loops.\n\n## Project structure:\n\n* src: Stores the code for the main pipeline, data extraction, processing, training, evaluation...\n* notebooks: Exploratory analyses in the form of jupyter notebooks.\n* seqloops: Boilerplate code and utilities meant to be imported as a python package.\n* scripts: various scripts that were used to generate the input data.\n\n\n## Setup:\n\nAll dependencies can be installed using:\n```bash\nmake deps\n```\n\nTo make `seqloops` importable in python scripts and notebooks, you can run: `make setup`.\n\nAll input and output data are managed via dvc. They can be imported as follows:\n```bash\npip install dvc[gdrive]\ndvc pull\n```\n\n## Workflow\n\nCode changes are managed via `git`. Data changes are managed via `dvc`, which is connected to a google drive folder.\nWhen modifying or adding new datafiles in the `data` folder, the modifications must be uploaded to the dvc server.\nThe updated small tracker file (`.dvc`) must be commited to git to keep track of changes.\nThe standard process is as follows:\n```bash\ndvc add data\ndvc push\ngit add data.dvc\ngit commit -m 'added new file'\ngit push\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Fsequence_loopability","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdoret%2Fsequence_loopability","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Fsequence_loopability/lists"}