{"id":24529026,"url":"https://github.com/saezlab/decoupler_manuscript","last_synced_at":"2025-10-07T02:55:25.411Z","repository":{"id":77872552,"uuid":"389940954","full_name":"saezlab/decoupleR_manuscript","owner":"saezlab","description":"Code to reproduce the results from decoupleR's manuscript","archived":false,"fork":false,"pushed_at":"2022-02-28T22:06:09.000Z","size":119,"stargazers_count":9,"open_issues_count":0,"forks_count":4,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-05T19:12:21.767Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/saezlab.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":"2021-07-27T10:28:56.000Z","updated_at":"2025-02-18T00:59:10.000Z","dependencies_parsed_at":"2023-03-04T02:45:45.215Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/decoupleR_manuscript","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/saezlab/decoupleR_manuscript","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR_manuscript","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR_manuscript/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR_manuscript/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR_manuscript/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/decoupleR_manuscript/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR_manuscript/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278712535,"owners_count":26032740,"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","status":"online","status_checked_at":"2025-10-07T02:00:06.786Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2025-01-22T07:34:28.657Z","updated_at":"2025-10-07T02:55:25.378Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# decoupleR_manuscript\nCode to reproduce the results from decoupleR's manuscript\n\n## Abstract\nComputational methods allow the extraction of mechanistic signatures from omics \ndata based on prior knowledge resources, reducing the dimensionality of the data\nfor increased statistical power and better interpretability. Here, we present \ndecoupleR, a Bioconductor package containing different statistical methods to \nextract these signatures within a unified framework. decoupleR allows the user \nto flexibly test any method with any resource. It incorporates methods that take\ninto account the sign and weight of network interactions. Using decoupleR, we \nevaluated the performance of contemporary methods on transcriptomic and \nphospho-proteomic perturbation experiments.\n\n## Benchmark pipeline\nIn this manuscript we have built a separate R package to benchmark decoupleR,\ncalled decoupleRBench. You can install it by running:\n```\ndevtools::install_github('saezlab/decoupleRBench')\n```\nYou can check the source code in: https://github.com/saezlab/decoupleRBench\n\n## Data\nTo retrieve all the necessary data, please run:\n```\nRscript R/process/get_data.R\n```\n\n## Analysis\nTo reproduce all the analyses performed in the manuscript, please run:\n```\n# Run perturbation benchmark\nRscript R/process/run_rna_bench.R\nRscript R/process/run_php_bench.R\n\n# Run noise analysis (This might take a while)\nRscript R/process/run_rna_noise.R #(~6 hours)\nRscript R/process/run_php_noise.R #(~2 hours)\n\n# Run scalablity analysis (This might take a while)\nRscript R/process/get_simmulated_data.R\nbash run_scale_bench.R\n```\n\n## Figures\nTo generate all the figures shown in the manuscript, please run:\n```\nRscript R/plot/supp_fig_1.R\nRscript R/plot/supp_fig_2.R\nRscript R/plot/supp_fig_3.R\nRscript R/plot/supp_fig_4.R\nRscript R/plot/supp_fig_5.R\nRscript R/plot/supp_fig_6.R\nRscript R/plot/supp_fig_7.R\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fdecoupler_manuscript","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fdecoupler_manuscript","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fdecoupler_manuscript/lists"}