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pareg

Pathway enrichment computations using a regularized regression approach to incorporate inter-pathway relations in the statistical model.

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

Science Score: 23.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages gene bioinformatics proteomics ontologies
Last synced: 11 months ago · JSON representation

Repository

Pathway enrichment computations using a regularized regression approach to incorporate inter-pathway relations in the statistical model.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Created about 7 years ago · Last pushed about 3 years ago
Metadata Files
Readme Changelog

README.md

pareg

lintr Mega-Linter check-bioc pkgdown BioC status

Pathway enrichment computations using a regularized regression approach to incorporate inter-pathway relations in the statistical model.

Installation

Install the latest stable version from Bioconductor: r BiocManager::install("pareg")

Install the latest development version from GitHub: r remotes::install_github("cbg-ethz/pareg")

Project structure

  • .: R package
  • inst/scripts/: Snakemake workflows and other utilities

Dev notes

  • Update NAMESPACE and write man pages: Rscript -e "devtools::document()"
  • Format code: Rscript -e "styler::style_dir('.', transformers = biocthis::bioc_style())"

Owner

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

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 641
  • Total Committers: 4
  • Avg Commits per committer: 160.25
  • Development Distribution Score (DDS): 0.016
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****i@g****m 631
J Wokaty j****y 4
mpirkl m****l@b****h 4
Nitesh Turaga n****a@g****m 2
Committer Domains (Top 20 + Academic)
bsse.ethz.ch: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 7
  • Total pull requests: 5
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 2 days
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 1.57
  • Average comments per pull request: 0.6
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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 (6)
  • HenrikBengtsson (1)
Pull Request Authors
  • kpj (5)
Top Labels
Issue Labels
bug (1) documentation (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,168 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: pareg

Pathway enrichment using a regularized regression approach

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,168 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 32.0%
Downloads: 95.9%
Maintainers (1)
kim.philipp.jablonski@gmail.com
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • tensorflow >= 2.2.0 depends
  • tfprobability >= 0.10.0 depends
  • DOSE * imports
  • Matrix * imports
  • devtools * imports
  • doFuture * imports
  • doRNG * imports
  • dplyr * imports
  • foreach * imports
  • future * imports
  • ggplot2 * imports
  • ggraph * imports
  • ggrepel * imports
  • glue * imports
  • hms * imports
  • igraph * imports
  • keras * imports
  • logger * imports
  • magrittr * imports
  • methods * imports
  • nloptr * imports
  • progress * imports
  • proxy * imports
  • purrr * imports
  • reticulate * imports
  • rlang * imports
  • stats * imports
  • stringr * imports
  • tibble * imports
  • tidygraph * imports
  • tidyr * imports
  • BiocParallel * suggests
  • BiocStyle * suggests
  • ComplexHeatmap * suggests
  • GGally * suggests
  • GO.db * suggests
  • GSEABenchmarkeR * suggests
  • PRROC * suggests
  • betareg * suggests
  • circlize * suggests
  • cowplot * suggests
  • enrichplot * suggests
  • fgsea * suggests
  • formatR * suggests
  • ggfittext * suggests
  • ggnewscale * suggests
  • ggsignif * suggests
  • ggupset * suggests
  • knitr * suggests
  • latex2exp * suggests
  • mgsa * suggests
  • msigdbr * suggests
  • org.Hs.eg.db * suggests
  • plotROC * suggests
  • rmarkdown * suggests
  • simplifyEnrichment * suggests
  • testthat >= 2.1.0 suggests
  • tidyverse * suggests
  • topGO * suggests
.github/workflows/check-bioc.yaml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/lintr.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/mega-linter.yaml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • megalinter/megalinter v5 composite
  • peter-evans/create-pull-request v3 composite
  • stefanzweifel/git-auto-commit-action v4 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite