# dce <img src="man/figures/logo.png" align="right" alt="dce logo" width="120" /> [](https://github.com/cbg-ethz/dce/actions) [](https://github.com/cbg-ethz/dce/actions) [](https://github.com/cbg-ethz/dce/actions) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/dce) Compute differential causal effects on (biological) networks. Check out [our vignettes](https://cbg-ethz.github.io/dce/articles/dce.html) for more information. > Publication: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab847/6470558 ## Installation Install the latest stable version from Bioconductor: ```r BiocManager::install("dce") ``` Install the latest development version from GitHub: ```r remotes::install_github("cbg-ethz/dce") ``` ## Project structure * `.`: R package * `inst/scripts/`: Snakemake workflows for all investigations in publication * `crispr_benchmark`: Real-life data validation * `gtex_validation`: Deconfounding validation * `ovarian_cancer`: How does Ovarian Cancer dysregulate pathways? * `synthetic_benchmark`: Synthetic data validation * `tcga_pipeline`: Compute effects for loads of data from TCGA ## Development notes * Check package locally: * `Rscript -e "lintr::lint_package()"` * `Rscript -e "devtools::test()"` * `Rscript -e "devtools::check(error_on = 'warning')"` * `R CMD BiocCheck` * Documentation * Build locally: `Rscript -e "pkgdown::build_site()"` * Deploy: `Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"` * Bioconductor * The `bioc` branch stores changes specific to Bioconductor releases * Update workflow (after `git remote add upstream git@git.bioconductor.org:packages/dce.git`): * `git checkout bioc` * `git merge master` * `git push upstream bioc:master`