{"id":24529086,"url":"https://github.com/saezlab/oncosignature","last_synced_at":"2025-07-30T19:05:09.844Z","repository":{"id":45714466,"uuid":"175004796","full_name":"saezlab/OncoSignature","owner":"saezlab","description":"Scripts used to perform the analyses of OncoSignature project for AML","archived":false,"fork":false,"pushed_at":"2022-07-15T08:59:08.000Z","size":237,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-22T07:37:40.183Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/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}},"created_at":"2019-03-11T13:21:45.000Z","updated_at":"2023-10-21T05:45:02.000Z","dependencies_parsed_at":"2022-09-24T05:12:14.794Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/OncoSignature","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOncoSignature","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOncoSignature/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOncoSignature/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FOncoSignature/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/OncoSignature/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243769949,"owners_count":20345215,"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":"2025-01-22T07:34:44.700Z","updated_at":"2025-03-15T17:45:15.375Z","avatar_url":"https://github.com/saezlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# OncoSignature - Drug response prediction on Acute Myeloid Leukemia\n\nCopyright (C) 2019 Nicolàs Palacio\u003cbr\u003e\nContact: nicolas.palacio@bioquant.uni-heidelberg.de\u003cbr\u003e  \nPlease, use the Github Issue page for questionts.\u003cbr\u003e  \n\nGNU-GLPv3:\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation.\n\nThis program is distributed in the hope that it will be useful, but\nWITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\nGeneral Public License for more details.\n\nA full copy of the GNU General Public License can be found on\nhttp://www.gnu.org/licenses/.\n\nThis repository contains the scripts used to analyze and extract\nphosphorylation signatures of drug response in AML samples.\n\n![Grapical abstract](oncosignature_pipeline.svg)\n\n## 1) Data normalization pipeline\nData cleaning + normalization + batch correction\n\n## 2) Differential expression analysis\nThis script analyzes the differential expression between treated vs. untreted\nsamples (responders and non-responders seperatedly) and between responders\nvs. non-responders before treatment\n\n### 2.1) Differential expression plots\nThis script generates the volcano plots to visualize the differential\nexpression results\n\n### 2.2) Biomarkers of interest\nThis script tries to find interesting biomarkers based on the differential\nexpression results. Phosphosites of interest are defined as follows:\n\n### 2.3) Significant differential phosphorylation\nThis script subsets the differential expresssion results and saves\na table for each contrast containing only the significantly\ndifferentially expressed p-sites.\n\n## 3) Gene Set Enrichment Analysis\nThis script computes the GSEA with 11 different methods and generates a\nconsensus score based on ranking\n\n### 3.1) Gene set enrichment analysis plots\nThis script generates the plots to visualize the results of the GSEA\n\n## 4) Kinase-substrate enrichment analysis\nThis script computes the kinase enrichment based on the differential\nphosphoproteomics data\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Foncosignature","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Foncosignature","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Foncosignature/lists"}