{"id":20751234,"url":"https://github.com/cbg-ethz/dce","last_synced_at":"2025-04-28T13:09:55.060Z","repository":{"id":42622334,"uuid":"193362564","full_name":"cbg-ethz/dce","owner":"cbg-ethz","description":"Finding the causality in biological pathways","archived":false,"fork":false,"pushed_at":"2023-07-12T07:56:17.000Z","size":13364,"stargazers_count":13,"open_issues_count":1,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-28T13:09:46.484Z","etag":null,"topics":["bioconductor","causality","r"],"latest_commit_sha":null,"homepage":"https://cbg-ethz.github.io/dce/","language":"R","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/cbg-ethz.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"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":"2019-06-23T15:09:49.000Z","updated_at":"2024-10-24T02:51:08.000Z","dependencies_parsed_at":"2024-11-17T23:18:05.722Z","dependency_job_id":null,"html_url":"https://github.com/cbg-ethz/dce","commit_stats":{"total_commits":910,"total_committers":6,"mean_commits":"151.66666666666666","dds":0.6175824175824176,"last_synced_commit":"af5757be224e05e43338421a2886f1dd6a63939f"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fdce","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fdce/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fdce/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fdce/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbg-ethz","download_url":"https://codeload.github.com/cbg-ethz/dce/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251319605,"owners_count":21570427,"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":["bioconductor","causality","r"],"created_at":"2024-11-17T08:32:00.908Z","updated_at":"2025-04-28T13:09:54.648Z","avatar_url":"https://github.com/cbg-ethz.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dce \u003cimg src=\"man/figures/logo.png\" align=\"right\" alt=\"dce logo\" width=\"120\" /\u003e\n\n[![lint](https://github.com/cbg-ethz/dce/workflows/lint/badge.svg)](https://github.com/cbg-ethz/dce/actions)\n[![check-bioc](https://github.com/cbg-ethz/dce/workflows/check-bioc/badge.svg)](https://github.com/cbg-ethz/dce/actions)\n[![pkgdown](https://github.com/cbg-ethz/dce/workflows/pkgdown/badge.svg)](https://github.com/cbg-ethz/dce/actions)\n[![BioC status](http://www.bioconductor.org/shields/build/devel/bioc/dce.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/dce)\n\nCompute differential causal effects on (biological) networks. Check out [our vignettes](https://cbg-ethz.github.io/dce/articles/dce.html) for more information.\n\n\u003e Publication: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab847/6470558\n\n## Installation\n\nInstall the latest stable version from Bioconductor:\n```r\nBiocManager::install(\"dce\")\n```\n\nInstall the latest development version from GitHub:\n```r\nremotes::install_github(\"cbg-ethz/dce\")\n```\n\n\n## Project structure\n\n* `.`: R package\n* `inst/scripts/`: Snakemake workflows for all investigations in publication\n    * `crispr_benchmark`: Real-life data validation\n    * `gtex_validation`: Deconfounding validation\n    * `ovarian_cancer`: How does Ovarian Cancer dysregulate pathways?\n    * `synthetic_benchmark`: Synthetic data validation\n    * `tcga_pipeline`: Compute effects for loads of data from TCGA\n\n\n## Development notes\n\n* Check package locally:\n    * `Rscript -e \"lintr::lint_package()\"`\n    * `Rscript -e \"devtools::test()\"`\n    * `Rscript -e \"devtools::check(error_on = 'warning')\"`\n    * `R CMD BiocCheck`\n* Documentation\n    * Build locally: `Rscript -e \"pkgdown::build_site()\"`\n    * Deploy: `Rscript -e \"pkgdown::deploy_to_branch(new_process = FALSE)\"`\n* Bioconductor\n    * The `bioc` branch stores changes specific to Bioconductor releases\n    * Update workflow (after `git remote add upstream git@git.bioconductor.org:packages/dce.git`):\n        * `git checkout bioc`\n        * `git merge master`\n        * `git push upstream bioc:master`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fdce","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbg-ethz%2Fdce","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fdce/lists"}