{"id":30348026,"url":"https://github.com/nuno-agostinho/ctrap","last_synced_at":"2025-08-18T17:30:34.588Z","repository":{"id":38409223,"uuid":"150247015","full_name":"nuno-agostinho/cTRAP","owner":"nuno-agostinho","description":"Identification of candidate causal perturbations from differential gene expression data","archived":false,"fork":false,"pushed_at":"2025-07-28T07:26:59.000Z","size":502485,"stargazers_count":6,"open_issues_count":4,"forks_count":1,"subscribers_count":1,"default_branch":"devel","last_synced_at":"2025-07-28T09:24:34.044Z","etag":null,"topics":["bioconductor","bioinformatics","cmap","gene-expression","l1000","r","r-package"],"latest_commit_sha":null,"homepage":"https://nuno-agostinho.github.io/cTRAP","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nuno-agostinho.png","metadata":{"files":{"readme":"README.md","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,"zenodo":null}},"created_at":"2018-09-25T10:23:35.000Z","updated_at":"2025-06-10T12:47:46.000Z","dependencies_parsed_at":"2023-10-02T08:40:25.322Z","dependency_job_id":"21edfa45-8a0e-4d64-9cf9-9abb0971e4c6","html_url":"https://github.com/nuno-agostinho/cTRAP","commit_stats":{"total_commits":341,"total_committers":4,"mean_commits":85.25,"dds":0.02639296187683282,"last_synced_commit":"491b0e9d41ddc313c3deb95b04fe84e9d44bc985"},"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/nuno-agostinho/cTRAP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuno-agostinho%2FcTRAP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuno-agostinho%2FcTRAP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuno-agostinho%2FcTRAP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuno-agostinho%2FcTRAP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nuno-agostinho","download_url":"https://codeload.github.com/nuno-agostinho/cTRAP/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuno-agostinho%2FcTRAP/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271029776,"owners_count":24687487,"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","status":"online","status_checked_at":"2025-08-18T02:00:08.743Z","response_time":89,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["bioconductor","bioinformatics","cmap","gene-expression","l1000","r","r-package"],"created_at":"2025-08-18T17:30:27.112Z","updated_at":"2025-08-18T17:30:34.510Z","avatar_url":"https://github.com/nuno-agostinho.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# cTRAP\n\n\u003c!-- badges: start --\u003e\n[![GitHub Actions Build status][ghActionsIcon]][ghActions]\n[![Coverage status][codecovBadge]][codecov]\n\u003c!-- badges: end --\u003e\n\n`cTRAP` is an R package designed to compare differential gene\nexpression results with those from known cellular perturbations (such as gene \nknock-down, overexpression or small molecules) derived from the \n[Connectivity Map][clue.io] [(Subramanian et al., Cell 2017)][subramanian2017].\nSuch analyses allow not only to infer the molecular causes of the observed \ndifference in gene expression but also to identify small molecules that could \ndrive or revert specific transcriptomic alterations.\n\n## Installing\n\n### Bioconductor\n\n[cTRAP is available in Bioconductor][bioconductor] and can be installed with:\n\n``` r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"cTRAP\")\n```\n\n### GitHub\n\ncTRAP can also be installed from GitHub instead:\n\n``` r\ninstall.packages(\"remotes\")\nremotes::install_github(\"nuno-agostinho/cTRAP\")\n```\n\n### Docker\n\nThe Docker images are based on [Bioconductor Docker][biocDocker] and contain cTRAP and its dependencies.\n\n1. Pull the latest Docker image:\n\n```\ndocker pull ghcr.io/nuno-agostinho/ctrap:latest\n```\n\n2. Start RStudio Web from the Docker image:\n\n```\ndocker run -e PASSWORD=bioc -p 8787:8787 ghcr.io/nuno-agostinho/ctrap:latest\n```\n\n3. Go to RStudio Web via your web browser at https://localhost:8787\n4. Login in RStudio Web with user `rstudio` and password `bioc`\n5. Load the package in RStudio Web using `library(cTRAP)`\n\n[clue.io]: https://clue.io/\n[subramanian2017]: https://doi.org/10.1016/j.cell.2017.10.049\n[codecov]: https://codecov.io/github/nuno-agostinho/cTRAP?branch=master\n[codecovBadge]: https://img.shields.io/codecov/c/github/nuno-agostinho/cTRAP/master.svg\n[ghActions]: https://github.com/nuno-agostinho/cTRAP/actions\n[ghActionsIcon]: https://github.com/nuno-agostinho/cTRAP/workflows/R-CMD-check-bioc/badge.svg\n[bioconductor]: http://bioconductor.org/packages/cTRAP\n[biocDocker]: https://github.com/Bioconductor/bioconductor_docker\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnuno-agostinho%2Fctrap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnuno-agostinho%2Fctrap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnuno-agostinho%2Fctrap/lists"}