Data

Tools

Indexes

Applications

Experiments

Open Source Science

BridgeDbR

Bioconductor R package for BridgeDb

https://github.com/bridgedb/bridgedbr

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 15 committers (13.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary

Keywords

bioconductor-package bridgedb genes identifiers life-sciences metabolites proteins

Keywords from Contributors

genomics bioinformatics bioconductor feature-detection mass-spectrometry metabolomics proteomics rnaseq peak-detection derfinder
Last synced: 6 months ago · JSON representation

Repository

Bioconductor R package for BridgeDb

Basic Info
Statistics
  • Stars: 4
  • Watchers: 8
  • Forks: 3
  • Open Issues: 14
  • Releases: 0
Fork of egonw/BridgeDbR
Topics
bioconductor-package bridgedb genes identifiers life-sciences metabolites proteins
Created over 8 years ago · Last pushed 7 months ago
Metadata Files
Readme

README.md

BioC Release Build Status - Bioconductor Release Build

BioC Dev Build Status - Bioconductor Dev Build

BridgeDbR package

R package for BridgeDb, a tool for identifier mapping.

Learn about BridgeDb at http://www.bridgedb.org/ and read about it in this paper:

Van Iersel, M.; Pico, A.; Kelder, T.; Gao, J.; Ho, I.; Hanspers, K.; Conklin, B.; Evelo, C. BMC Bioinformatics 2010, 11, 5, https://doi.org/10.1186/1471-2105-11-5

The DOI of this package is https://doi.org/10.18129/B9.bioc.BridgeDbR

The source code of this package is available from https://github.com/bridgedb/BridgeDbR

License: AGPL-3

Available from Bioconductor

To install this package, start R and enter:

install.packages("BiocManager") BiocManager::install("BridgeDbR")

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BridgeDbR")

http://www.bioconductor.org/packages/release/bioc/html/BridgeDbR.html

Compiling and Installing

To compile and install the lastest version from GitHub, or to test your patches, use the following commands:

R CMD build BridgeDbR
R CMD check BridgeDbR_x.y.z.tar.gz
R CMD INSTALL BridgeDbR_x.y.z.tar.gz

To create the vignette:

rm -f BridgeDbR/inst/doc/tutorial.pdf; R CMD build BridgeDbR; tar xvf BridgeDbR_0.99.1.tar.gz BridgeDbR/inst/doc/tutorial.pdf

To install the packages from within R with the devtools package:

> install.packages("rJava") # if not present already
> install.packages("curl") # if not present already
> install.packages("devtools") # if not present already
> library(devtools)
> install_github("bridgedb/BridgeDbR")

Dependencies

This package requires curl and RJava, which can be installed with:

install.packages(pkgs=c("rJava", "curl"))

Owner

  • Name: BridgeDb
  • Login: bridgedb
  • Kind: organization
  • Location: Netherlands

GitHub Events

Total
  • Push event: 2
Last Year
  • Push event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 157
  • Total Committers: 15
  • Avg Commits per committer: 10.467
  • Development Distribution Score (DDS): 0.312
Past Year
  • Commits: 34
  • Committers: 3
  • Avg Commits per committer: 11.333
  • Development Distribution Score (DDS): 0.118
Top Committers
Name Email Commits
Egon Willighagen e****n@g****m 108
Nitesh Turaga n****a@g****m 14
Dan Tenenbaum d****a@f****g 8
Tooba Abbassi-Daloii 3****i 5
Herve Pages h****s@f****g 4
Hervé Pagès h****s@f****g 3
De d****r@m****l 3
vobencha v****n@r****g 2
vobencha v****a@g****m 2
J Wokaty j****y 2
J Wokaty j****y@s****u 2
Hervé Pagès h****b@g****m 1
Marc Carlson m****n@f****g 1
sneumann s****n@i****e 1
Lori Shepherd l****d@r****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 2 ipb-halle.de: 1 sph.cuny.edu: 1 maastrichtuniversity.nl: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 24
  • Total pull requests: 8
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 8
  • Total pull request authors: 2
  • Average comments per issue: 1.88
  • Average comments per pull request: 1.0
  • Merged pull requests: 6
  • 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
  • egonw (12)
  • DeniseSl22 (6)
  • pporrasebi (1)
  • ariutta (1)
  • ff98li (1)
  • kozo2 (1)
  • lucas-ubm (1)
Pull Request Authors
  • tabbassidaloii (5)
  • DeniseSl22 (3)
Top Labels
Issue Labels
enhancement (8) bug (3) help wanted (1) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 23,301 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: BridgeDbR

Code for using BridgeDb identifier mapping framework from within R

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 23,301 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 14.4%
Average: 15.7%
Stargazers count: 19.5%
Downloads: 44.4%
Maintainers (1)
egon.willighagen@gmail.com
Last synced: 6 months ago