{"id":18501586,"url":"https://github.com/const-ae/proda-paper","last_synced_at":"2026-01-25T01:02:47.742Z","repository":{"id":82391885,"uuid":"189968873","full_name":"const-ae/proDA-Paper","owner":"const-ae","description":null,"archived":false,"fork":false,"pushed_at":"2020-04-30T10:56:37.000Z","size":69569,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-10T05:34:46.282Z","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":null,"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":null,"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":"2019-06-03T08:50:13.000Z","updated_at":"2024-09-19T10:18:47.000Z","dependencies_parsed_at":"2023-04-19T23:32:03.830Z","dependency_job_id":null,"html_url":"https://github.com/const-ae/proDA-Paper","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/const-ae/proDA-Paper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FproDA-Paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FproDA-Paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FproDA-Paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FproDA-Paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/proDA-Paper/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FproDA-Paper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28740399,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-24T22:12:27.248Z","status":"ssl_error","status_checked_at":"2026-01-24T22:12:10.529Z","response_time":89,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":"2024-11-06T13:54:21.267Z","updated_at":"2026-01-25T01:02:43.638Z","avatar_url":"https://github.com/const-ae.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# proDA-Paper\n\nCurrently available as a preprint:\n\nConstantin Ahlmann-Eltze and Simon Anders: *proDA: Probabilistic Dropout Analysis for Identifying Differentially Abundant Proteins in Label-Free Mass Spectrometry*. [biorXiv 661496](http://www.biorxiv.org/content/10.1101/661496v1) (Jun 2019)\n\n\nThis repository contains the code to reproduce the figures for the paper describing the \n[proDA](https://github.com/const-ae/proDA) R package.\n\n## Data\n\nThere are two datasets that are used for demonstration:\n\n* Data on the phosphorylation dynamics from a study by Erik de Graaf et al.\u003csup\u003e[1](#myfootnote1)\u003c/sup\u003e\n* Data studying the interaction landscape of Ubiquitin signalling by Xiaofei Zhang et al.\u003csup\u003e[2](#myfootnote2)\u003c/sup\u003e\n\nBoth can be found in the `data/` folder.\n\n## Analysis\n\nThere are three additional folders that contain R markdown notebook that were used to generate the plots\nfor the paper:\n\n* `approach_intuition` contains the code to give an overview of the ideas underlying `proDA`\n    - [Mean-variance relation](https://htmlpreview.github.io/?https://github.com/const-ae/proDA-Paper/blob/master/approach_intuition/mean_variance_relation.nb.html)\n    - [Location of missing values](https://htmlpreview.github.io/?https://github.com/const-ae/proDA-Paper/blob/master/approach_intuition/missing_value_location.nb.html)\n    - [Probabilistic dropout model](https://htmlpreview.github.io/?https://github.com/const-ae/proDA-Paper/blob/master/approach_intuition/probabilistic_dropout_model.nb.html)\n* `compare_performance` contains the code to run `DEP`, `QPROT`, `Perseus`, `DAPAR`, `EBRCT`,\n   `Triqler` and `proDA` on the\n  de Graaf data and make the validation and comparison plots\n    - Null comparison on the de Graaf data set [notebook](http://htmlpreview.github.io/?https://github.com/const-ae/proDA-Paper/blob/master/compare_performance/null_comparison.nb.html)\n    - de Graaf semi-synthetic dataset performance comparison [notebook](https://htmlpreview.github.io/?https://github.com/const-ae/proDA-Paper/blob/master/compare_performance/compare_performance.nb.html)\n* `ubiquitination` contains the code that was used to analyze the Ubiquitination data\n    - [Analysis notebook](https://htmlpreview.github.io/?https://github.com/const-ae/proDA-Paper/blob/master/ubiquitination/Ubiquitination_Analysis.nb.html)\n\n\n\n## Sources\n\n\u003ca name=\"myfootname1\"\u003e1.\u003c/a\u003e de Graaf, E. L., Giansanti, P., Altelaar, A. F. M. \u0026 Heck, A. J. R. Single-step Enrichment by Ti4 + -IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution . Mol. Cell. Proteomics 13, 2426–2434 (2014).\n\n\u003ca name=\"myfootname2\"\u003e2.\u003c/a\u003e Zhang, X. et al. An Interaction Landscape of Ubiquitin Signaling. Mol. Cell 65, 941–955.e8 (2017).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fproda-paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Fproda-paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fproda-paper/lists"}