https://github.com/cbg-ethz/dce

Finding the causality in biological pathways
https://github.com/cbg-ethz/dce

bioconductor causality r

Last synced: about 1 month ago
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Finding the causality in biological pathways

• Host: GitHub
• URL: https://github.com/cbg-ethz/dce
• Owner: cbg-ethz
• Created: 2019-06-23T15:09:49.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-07-12T07:56:17.000Z (almost 2 years ago)
• Last Synced: 2025-04-28T13:09:46.484Z (about 1 month ago)
• Topics: bioconductor, causality, r
• Language: R
• Homepage: https://cbg-ethz.github.io/dce/
• Size: 12.7 MB
• Stars: 13
• Watchers: 4
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

        
# dce 

[![lint](https://github.com/cbg-ethz/dce/workflows/lint/badge.svg)](https://github.com/cbg-ethz/dce/actions)

[![check-bioc](https://github.com/cbg-ethz/dce/workflows/check-bioc/badge.svg)](https://github.com/cbg-ethz/dce/actions)

[![pkgdown](https://github.com/cbg-ethz/dce/workflows/pkgdown/badge.svg)](https://github.com/cbg-ethz/dce/actions)

[![BioC status](http://www.bioconductor.org/shields/build/devel/bioc/dce.svg)](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 [email protected]:packages/dce.git`):

        * `git checkout bioc`

        * `git merge master`

        * `git push upstream bioc:master`