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msigdbr

MSigDB gene sets for multiple organisms in a tidy data format

https://github.com/igordot/msigdbr

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
    Found .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 (6.5%) to scientific vocabulary

Keywords

enrichment-analysis gene-sets genomics gsea msigdb pathway-analysis pathways
Last synced: 6 months ago · JSON representation

Repository

MSigDB gene sets for multiple organisms in a tidy data format

Basic Info
Statistics
  • Stars: 81
  • Watchers: 8
  • Forks: 15
  • Open Issues: 1
  • Releases: 15
Topics
enrichment-analysis gene-sets genomics gsea msigdb pathway-analysis pathways
Created almost 8 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

msigdbr: MSigDB data frame

CRAN CRAN downloads R-CMD-check Codecov test coverage

The msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets:

  • in an R-friendly tidy format with one gene pair per row
  • for multiple frequently studied model organisms in addition to the original human genes
  • as gene symbols as well as NCBI Entrez and Ensembl IDs
  • without accessing external resources requiring an active internet connection

Check the documentation website for more information.

Owner

  • Name: igor
  • Login: igordot
  • Kind: user
  • Location: New York, NY, USA
  • Company: New York University School of Medicine

GitHub Events

Total
  • Create event: 7
  • Release event: 7
  • Issues event: 26
  • Watch event: 10
  • Issue comment event: 31
  • Push event: 134
  • Pull request event: 2
  • Fork event: 1
Last Year
  • Create event: 7
  • Release event: 7
  • Issues event: 26
  • Watch event: 10
  • Issue comment event: 31
  • Push event: 134
  • Pull request event: 2
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 57
  • Total Committers: 4
  • Avg Commits per committer: 14.25
  • Development Distribution Score (DDS): 0.211
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
igor 6****t@u****m 45
igor i****t@u****m 10
Steve Ped s****n@a****u 1
Vince v****r@u****m 1
Committer Domains (Top 20 + Academic)
adelaide.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 44
  • Total pull requests: 8
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 1 year
  • Total issue authors: 42
  • Total pull request authors: 5
  • Average comments per issue: 2.43
  • Average comments per pull request: 1.88
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 16
  • Pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 15
  • Pull request authors: 0
  • Average comments per issue: 1.88
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • millerh1 (2)
  • assaron (2)
  • tuhulab (1)
  • agdenadel (1)
  • acaulier (1)
  • rebeelouise (1)
  • thommohr (1)
  • niuniudevp (1)
  • HamidKianGaikani (1)
  • kokitsuyuzaki (1)
  • dereckmezquita (1)
  • lxhuang7 (1)
  • coralzhang (1)
  • mw55309 (1)
  • lianos (1)
Pull Request Authors
  • ozturan (3)
  • TylerSagendorf (2)
  • jliu678 (1)
  • vreuter (1)
  • smped (1)
Top Labels
Issue Labels
enhancement (16) question (15) bug (8) duplicate (1) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 15,005 last-month
  • Total docker downloads: 26,163
  • Total dependent packages: 13
    (may contain duplicates)
  • Total dependent repositories: 68
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 1
cran.r-project.org: msigdbr

MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format

  • Versions: 13
  • Dependent Packages: 13
  • Dependent Repositories: 66
  • Downloads: 15,005 Last month
  • Docker Downloads: 26,163
Rankings
Dependent repos count: 3.0%
Dependent packages count: 4.3%
Stargazers count: 5.6%
Forks count: 5.8%
Downloads: 5.8%
Average: 7.5%
Docker downloads count: 20.2%
Maintainers (1)
igor.dolgalev@nyumc.org
Last synced: 6 months ago
conda-forge.org: r-msigdbr
  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 2
Rankings
Dependent repos count: 20.2%
Average: 38.4%
Stargazers count: 38.9%
Forks count: 42.7%
Dependent packages count: 51.6%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • babelgene * imports
  • dplyr >= 0.7.0 imports
  • magrittr * imports
  • rlang * imports
  • tibble * imports
  • tidyselect * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite