{"id":24528923,"url":"https://github.com/saezlab/progeny","last_synced_at":"2025-04-06T11:09:47.080Z","repository":{"id":24996621,"uuid":"67710487","full_name":"saezlab/progeny","owner":"saezlab","description":"R package for Pathway RespOnsive GENe activity inference","archived":false,"fork":false,"pushed_at":"2023-01-30T10:01:10.000Z","size":50183,"stargazers_count":101,"open_issues_count":3,"forks_count":20,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-03-30T10:07:02.483Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://saezlab.github.io/progeny/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","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":"2016-09-08T14:29:06.000Z","updated_at":"2025-03-24T13:19:07.000Z","dependencies_parsed_at":"2023-02-16T06:16:02.969Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/progeny","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprogeny","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprogeny/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprogeny/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fprogeny/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/progeny/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247471521,"owners_count":20944158,"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":"2025-01-22T07:33:59.852Z","updated_at":"2025-04-06T11:09:47.061Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PROGENy: Pathway RespOnsive GENes for activity inference \u003cimg src=\"man/figures/tool_logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n![GitHub](https://img.shields.io/github/license/saezlab/progeny)\n\u003c!-- badges: end --\u003e\n\n\n## Overview\n\nPROGENy is resource that leverages a large compendium of publicly available\nsignaling perturbation experiments to yield a common core of pathway responsive\ngenes for human and mouse. These, coupled with any statistical method, can be\nused to infer pathway activities from bulk or single-cell transcriptomics. \n\nThis is an R package for storing the pathway signatures. To infer pathway\nactivities, please check out\n[decoupleR](https://doi.org/10.1093/bioadv/vbac016), available in\n[R](https://saezlab.github.io/decoupleR/) or\n[python](https://github.com/saezlab/decoupler-py).\n\n## Installation\n\nProgeny is available in\n[Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/progeny.html). \nIn addition, one can install the development version from the Github repository: \n\n```r\n## To install the package from Bioconductor\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"progeny\")\n\n## To install the development version from the Github repo:\ndevtools::install_github(\"saezlab/progeny\")\n```\n\n## Updates\n\nSince the original release, we have implemented some extensions in PROGENy:\n\n1. **Extension to mouse**:\n  Originally PROGENy was developed for the application to human data. \n  In a benchmark study we showed that PROGENy is also applicable to mouse data, \n  as described in \n  [Holland et al., 2019](https://doi.org/10.1016/j.bbagrm.2019.194431). \n  Accordingly, we included new parameters to run mouse version of PROGENy by \n  transforming the human genes to their mouse orthologs.\n2. **Expanding Pathway Collection**:\n  We expanded human and mouse PROGENy with the pathways Androgen, Estrogen and \n  WNT.\n3. **Extension to single-cell RNA-seq data**:\n  We showed that PROGENy can be applied to scRNA-seq data, as described in\n  [Holland et al., 2020](https://doi.org/10.1186/s13059-020-1949-z)\n\n## Citation\n\n\u003e Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, \nBlüthgen N, Saez-Rodriguez J. 2018. Perturbation-response genes reveal signaling\nfootprints in cancer gene expression. _Nature Communications_: \n[10.1038/s41467-017-02391-6](https://doi.org/10.1038/s41467-017-02391-6)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fprogeny","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fprogeny","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fprogeny/lists"}