GitHub - cbg-ethz/dce: Finding the causality in biological pathways (original) (raw)

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• README

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 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