GitHub - cbg-ethz/dce: Finding the causality in biological pathways (original) (raw)
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dce 
Compute differential causal effects on (biological) networks. Check out our vignettes 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:
BiocManager::install("dce")
Install the latest development version from GitHub:
remotes::install_github("cbg-ethz/dce")
Project structure
.
: R packageinst/scripts/
: Snakemake workflows for all investigations in publicationcrispr_benchmark
: Real-life data validationgtex_validation
: Deconfounding validationovarian_cancer
: How does Ovarian Cancer dysregulate pathways?synthetic_benchmark
: Synthetic data validationtcga_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)"
- Build locally:
- 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
- The