{"id":24659929,"url":"https://github.com/saezlab/decoupleR","last_synced_at":"2025-10-07T21:32:09.351Z","repository":{"id":40414755,"uuid":"223271963","full_name":"saezlab/decoupleR","owner":"saezlab","description":"R package to infer biological activities from omics data using a collection of methods.","archived":false,"fork":false,"pushed_at":"2024-10-19T13:09:49.000Z","size":40359,"stargazers_count":218,"open_issues_count":6,"forks_count":24,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-01-22T07:37:23.607Z","etag":null,"topics":["r","r-package","rstats"],"latest_commit_sha":null,"homepage":"https://saezlab.github.io/decoupleR/","language":"R","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.Rmd","changelog":"NEWS.md","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":"2019-11-21T21:51:19.000Z","updated_at":"2025-01-15T13:26:12.000Z","dependencies_parsed_at":"2024-02-07T10:28:12.935Z","dependency_job_id":"b21edad6-6919-4564-8006-0b7ef74d3e8e","html_url":"https://github.com/saezlab/decoupleR","commit_stats":{"total_commits":644,"total_committers":17,"mean_commits":37.88235294117647,"dds":0.6987577639751552,"last_synced_commit":"dd9d47ea884570977fc88f8d10a579d40921b9a5"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FdecoupleR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/decoupleR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":235658573,"owners_count":19025084,"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":["r","r-package","rstats"],"created_at":"2025-01-26T03:01:54.627Z","updated_at":"2025-10-07T21:32:03.926Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":["R"],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n    collapse = TRUE,\n    comment = \"#\u003e\",\n    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# decoupleR \u003cimg src=\"inst/figures/logo.svg\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)\n[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/decoupleR.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/decoupleR)\n[![BioC dev status](http://www.bioconductor.org/shields/build/devel/bioc/decoupleR.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/decoupleR)\n[![R build status](https://github.com/saezlab/decoupleR/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/saezlab/decoupleR/actions)\n[![Codecov test coverage](https://codecov.io/gh/saezlab/decoupleR/branch/master/graph/badge.svg)](https://codecov.io/gh/saezlab/decoupleR?branch=master)\n[![GitHub issues](https://img.shields.io/github/issues/saezlab/decoupleR)](https://github.com/saezlab/decoupleR/issues)\n\u003c!-- badges: end --\u003e\n\n## Overview\n\nThere are many methods that allow us to extract biological activities from omics data. \n`decoupleR` is a Bioconductor package containing different statistical methods to \nextract biological signatures from prior knowledge within a unified framework.\nAdditionally, it incorporates methods that take into account the sign and weight of \nnetwork interactions. `decoupleR` can be used with any omic, as long as its \nfeatures can be linked to a biological process based on prior knowledge. \nFor example, in transcriptomics gene sets regulated by a transcription \nfactor, or in phospho-proteomics phosphosites that are targeted by a kinase.\nThis is the R version, for its faster and memory efficient Python implementation go [here](https://decoupler-py.readthedocs.io/en/latest/).\n\n\u003cp align=\"center\" width=\"100%\"\u003e\n    \u003cimg src=\"https://github.com/saezlab/decoupleR/blob/master/inst/figures/graphical_abstract.png?raw=1\" align=\"center\" width=\"45%\"\u003e\n\u003c/p\u003e\n\nFor more information about how this package has been used with real data,\nplease check the following links:\n\n- [decoupleR's general usage](https://saezlab.github.io/decoupleR/articles/decoupleR.html)\n- [Pathway activity inference in bulk RNA-seq](https://saezlab.github.io/decoupleR/articles/pw_bk.html)\n- [Pathway activity inference from scRNA-seq](https://saezlab.github.io/decoupleR/articles/pw_sc.html)\n- [Transcription factor activity inference in bulk RNA-seq](https://saezlab.github.io/decoupleR/articles/tf_bk.html)\n- [Transcription factor activity inference from scRNA-seq](https://saezlab.github.io/decoupleR/articles/tf_sc.html)\n- [Example of Kinase and TF activity estimation](https://saezlab.github.io/kinase_tf_mini_tuto/)\n- [decoupleR's manuscript repository](https://github.com/saezlab/decoupleR_manuscript)\n- [Python implementation](https://decoupler-py.readthedocs.io/en/latest/)\n\n# Installation\n`decoupleR` is an R package distributed as part of the Bioconductor\nproject. To install the package, start R and enter:\n\n```{r bioconductor_install, eval=FALSE}\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"decoupleR\")\n```\n\nAlternatively, you can instead install the latest development version from [GitHub](https://github.com/) with:\n\n```{r github_install, eval=FALSE}\nBiocManager::install(\"saezlab/decoupleR\")\n```\n\n## License\nFootprint methods inside `decoupleR` can be used for academic or commercial purposes, except `viper` which holds a non-commercial license. \n\nThe data redistributed by `OmniPath` does not have a license, each original resource carries their own. \n[Here](https://omnipathdb.org/info) one can find the license information of all the resources in `OmniPath`.\n\n## Citation\nBadia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov D., Müller-Dott S., Taus P., Dugourd A., Holland\nC.H., Ramirez Flores R.O.  and Saez-Rodriguez J. 2022. decoupleR: ensemble of computational methods to infer\nbiological activities from omics data. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbac016\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2FdecoupleR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2FdecoupleR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2FdecoupleR/lists"}