{"id":13755644,"url":"https://github.com/shtoneyan/gopher","last_synced_at":"2026-01-14T07:58:07.279Z","repository":{"id":38534510,"uuid":"457950332","full_name":"shtoneyan/gopher","owner":"shtoneyan","description":"Toolset for training quantitative sequence to function models.","archived":false,"fork":false,"pushed_at":"2024-03-15T17:03:12.000Z","size":90682,"stargazers_count":23,"open_issues_count":1,"forks_count":10,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-11-07T04:14:28.310Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/shtoneyan.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":"2022-02-10T21:17:14.000Z","updated_at":"2025-03-04T12:15:40.000Z","dependencies_parsed_at":"2024-01-17T15:04:28.168Z","dependency_job_id":"9a421bec-69f3-4233-876a-92280b2f1eb0","html_url":"https://github.com/shtoneyan/gopher","commit_stats":{"total_commits":231,"total_committers":4,"mean_commits":57.75,"dds":0.5021645021645021,"last_synced_commit":"ddde0f744991b3a9d9c4ecc45b73ad709544906e"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/shtoneyan/gopher","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shtoneyan%2Fgopher","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shtoneyan%2Fgopher/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shtoneyan%2Fgopher/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shtoneyan%2Fgopher/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/shtoneyan","download_url":"https://codeload.github.com/shtoneyan/gopher/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/shtoneyan%2Fgopher/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28413527,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T05:26:33.345Z","status":"ssl_error","status_checked_at":"2026-01-14T05:21:57.251Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2024-08-03T11:00:17.648Z","updated_at":"2026-01-14T07:58:07.259Z","avatar_url":"https://github.com/shtoneyan.png","language":"Jupyter Notebook","funding_links":[],"categories":["Software packages"],"sub_categories":["DL4G Packages"],"readme":"\n\u003cimg src=\"./DALL·E 2022-10-05 14.40.17 - Constellation in a shape of groundhog. graphical art.png\" width=\"100\" height='100'\u003e\n\n**GOPHER**: **G**en**O**mic **P**rofile-model compre**H**ensive **E**valuato**R**\n\n## Installation\n\n```\n$ pip install bio-gopher\n```\nNote that for proper installation, numpy needs to be installed before pyBigWig.\n\nThis repository contains scripts for data preprocessing, training deep learning models for DNA sequence to epigenetic function prediction and evaluation of models.\n\nThe repo contains a set of tutorial jupyter notebooks that illustrate these steps on a toy dataset. The two notebooks below are required prerequisites for the rest of tutorials:\n- preprocessing/preprocessing/quant_dataset_tutorial.ipynb\n- tutorials/train_model.ipynb\n\n\nTo replicate the results of the manuscript run the scripts in the analyzis directory. As a prerequisite download and unzip dataset.zip, trained_models.zip from zenodo https://doi.org/10.5281/zenodo.6464031 within the git repo. These contain test sets and pre-trained models. The analysis scripts can be ran in any order as long as paper_run_evaluate.py is ran first, in order to produce model evaluations which is required for further steps.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshtoneyan%2Fgopher","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fshtoneyan%2Fgopher","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshtoneyan%2Fgopher/lists"}