{"id":24528981,"url":"https://github.com/saezlab/factor_cosmos","last_synced_at":"2026-01-02T16:46:39.029Z","repository":{"id":43177020,"uuid":"463073255","full_name":"saezlab/Factor_COSMOS","owner":"saezlab","description":"Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.","archived":false,"fork":false,"pushed_at":"2024-07-10T11:18:35.000Z","size":163457,"stargazers_count":8,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-01-22T07:37:26.967Z","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/saezlab.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":"support/c2.cp.v2022.1.Hs.symbols.gmt","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-02-24T08:49:43.000Z","updated_at":"2024-12-13T16:17:55.000Z","dependencies_parsed_at":"2024-07-10T13:25:09.841Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/Factor_COSMOS","commit_stats":null,"previous_names":["saezlab/factor_cosmos"],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FFactor_COSMOS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FFactor_COSMOS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FFactor_COSMOS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FFactor_COSMOS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/Factor_COSMOS/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243769947,"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":"2025-01-22T07:34:16.229Z","updated_at":"2026-01-02T16:46:39.000Z","avatar_url":"https://github.com/saezlab.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NCI60_mofa_cosmos\n\nTutorial on how to use the MOFA-COSMOS pipeline in order to generate testable hypothesis connecting MOFA outputs with COSMOS network inference. This tutorial is especially targeted at dataset that span transcriptomic, proteomic and metabolomic. \n\nIf you want to see how to integrate phospho-proteomic and transcriptomic data, or if you are only interested in MOON, you can find a specifically tailored tutorial for that here: https://github.com/saezlab/MOON_example\n\n## Install cosmosR\nR \u003e= 4.1 is required\n```r\nif (!requireNamespace(\"devtools\", quietly = TRUE))\n    install.packages(\"devtools\")\n    \ndevtools::install_github(\"saezlab/cosmosR\")\n```\n\n## TLDR:\nThe main pipleine script with all explanations can be found in this repository: MOFA_to_COSMOS.md (https://github.com/saezlab/Factor_COSMOS/blob/main/MOFA_to_COSMOS.md)\n\nSample specific analysis can be found in: Cell_line_MOFA_space.md (https://github.com/saezlab/Factor_COSMOS/blob/main/Cell_line_MOFA_space.md)\n\nPathway control analysis can be found in: pathway_control_analysis_moon.md (https://github.com/saezlab/Factor_COSMOS/blob/main/pathway_control_analysis_moon.md)\n\n## If you wish to run it locally:\n\nClone the repository locally\n\nopen NCI60.Rproj with Rstudio (then all the file path should be properlly working)\n\nOpen the .rmd file you are interested in (ex: MOFA_to_COSMOS.rmd)\n\nOnce the required packages are installed, and MOFA is set up with python, everything should run smoothly\n\n(If you wish to run the part of COSMOS that relied on CARNIVAL, you will need to install the cplex IBM solver too and set the path in the script)\n\nPlease cite: https://www.embopress.org/doi/full/10.15252/msb.20209730\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Ffactor_cosmos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Ffactor_cosmos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Ffactor_cosmos/lists"}