Data

Tools

Indexes

Applications

Experiments

Open Source Science

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

Finding the causality in biological pathways

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

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary

Keywords

bioconductor causality r
Last synced: 5 months ago · JSON representation

Repository

Finding the causality in biological pathways

Basic Info
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 3
  • Open Issues: 1
  • Releases: 0
Topics
bioconductor causality r
Created over 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog

README.md

dce dce logo

lint check-bioc pkgdown BioC status

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: 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

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 910
  • Total Committers: 5
  • Avg Commits per committer: 182.0
  • Development Distribution Score (DDS): 0.286
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kpj k****j@g****m 650
mpirkl m****l@b****h 208
mpirkl m****l@y****e 38
Domagoj Cevid c****d@s****h 12
Domagoj Ćevid d****d 2
Committer Domains (Top 20 + Academic)
stat.math.ethz.ch: 1 yahoo.de: 1 bsse.ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 28
  • Total pull requests: 11
  • Average time to close issues: 7 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 4
  • Total pull request authors: 3
  • Average comments per issue: 2.14
  • Average comments per pull request: 0.91
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kpj (16)
  • MartinFXP (8)
  • Miaoxingzi (1)
  • dcevid (1)
Pull Request Authors
  • MartinFXP (5)
  • dcevid (3)
  • kpj (3)
Top Labels
Issue Labels
enhancement (4) bug (2) help wanted (1) wontfix (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,667 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: dce

Pathway Enrichment Based on Differential Causal Effects

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,667 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 26.8%
Downloads: 80.3%
Maintainers (1)
kim.philipp.jablonski@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • MASS * imports
  • Matrix * imports
  • Rgraphviz * imports
  • assertthat * imports
  • dplyr * imports
  • edgeR * imports
  • epiNEM * imports
  • expm * imports
  • ggplot2 * imports
  • ggraph * imports
  • glm2 * imports
  • glue * imports
  • graph * imports
  • graphite * imports
  • harmonicmeanp * imports
  • igraph * imports
  • logger * imports
  • magrittr * imports
  • metap * imports
  • methods * imports
  • mnem * imports
  • naturalsort * imports
  • org.Hs.eg.db * imports
  • pcalg * imports
  • ppcor * imports
  • purrr * imports
  • reshape2 * imports
  • rlang * imports
  • shadowtext * imports
  • stats * imports
  • tidygraph * imports
  • tidyverse * imports
  • BiocStyle * suggests
  • CARNIVAL * suggests
  • RcppParallel * suggests
  • SummarizedExperiment * suggests
  • TCGAutils * suggests
  • cowplot * suggests
  • curatedTCGAData * suggests
  • dagitty * suggests
  • devtools * suggests
  • docopt * suggests
  • formatR * suggests
  • ggplotify * suggests
  • knitr * suggests
  • lmtest * suggests
  • rmarkdown * suggests
  • sandwich * suggests
  • testthat >= 2.1.0 suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
.github/workflows/linter.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite