{"id":18501593,"url":"https://github.com/const-ae/linear_perturbation_prediction-paper","last_synced_at":"2026-01-24T15:35:09.669Z","repository":{"id":257493350,"uuid":"848734971","full_name":"const-ae/linear_perturbation_prediction-Paper","owner":"const-ae","description":null,"archived":false,"fork":false,"pushed_at":"2025-07-18T11:54:44.000Z","size":63799,"stargazers_count":49,"open_issues_count":1,"forks_count":9,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-09-10T05:34:08.463Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/const-ae.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-08-28T10:05:11.000Z","updated_at":"2025-09-01T11:17:37.000Z","dependencies_parsed_at":null,"dependency_job_id":"aa4dfdcb-cda2-4c99-ba3b-69dfdda76ad0","html_url":"https://github.com/const-ae/linear_perturbation_prediction-Paper","commit_stats":null,"previous_names":["const-ae/linear_perturbation_prediction-paper"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/const-ae/linear_perturbation_prediction-Paper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2Flinear_perturbation_prediction-Paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2Flinear_perturbation_prediction-Paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2Flinear_perturbation_prediction-Paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2Flinear_perturbation_prediction-Paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/linear_perturbation_prediction-Paper/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2Flinear_perturbation_prediction-Paper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28730322,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-24T10:24:43.181Z","status":"ssl_error","status_checked_at":"2026-01-24T10:24:36.112Z","response_time":89,"last_error":"SSL_read: 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":"2024-11-06T13:54:22.030Z","updated_at":"2026-01-24T15:35:09.664Z","avatar_url":"https://github.com/const-ae.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Code repository for *Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear baselines*\n\nThis repository contains the code to reproduce our analysis from\n\n\u003e Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear baselines. \nConstantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders.\n_Nature Methods_ 2025; doi: https://doi.org/10.1038/s41592-025-02772-6\n\nA copy of the code is permanently archived at https://doi.org/10.5281/zenodo.14832393.\n\n- The **notebooks** folder contains the R scripts used for the analysis and to make the figures\n  - [Double Perturbation Analysis](https://htmlpreview.github.io/?https://github.com/const-ae/linear_perturbation_prediction-Paper/blob/main/notebooks/double_perturbation_analysis.html)\n  - [Single Perturbation Analysis](https://htmlpreview.github.io/?https://github.com/const-ae/linear_perturbation_prediction-Paper/blob/main/notebooks/single_perturbation_analysis.html)\n  - [Dataset Overview](https://htmlpreview.github.io/?https://github.com/const-ae/linear_perturbation_prediction-Paper/blob/main/notebooks/dataset_overview.html)\n- The **benchmark** folder contains the scripts to reproduce the benchmark results\n  - The **benchmark/src** contains individual scripts to run each method\n  - The **benchmark/conda_environments** and **benchmark/renv** contain the details about the software versions\n  - The **benchmark/submission** contains the script to launch the scripts using my [custom](https://github.com/const-ae/MyWorkflowManager) workflow manager\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Flinear_perturbation_prediction-paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Flinear_perturbation_prediction-paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Flinear_perturbation_prediction-paper/lists"}