Data

Tools

Indexes

Applications

Experiments

Open Source Science

MsBackendMassbank

A prototype backend to parse MassBank records into Spectra

https://github.com/rformassspectrometry/msbackendmassbank

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
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords

massbank spectra

Keywords from Contributors

bioconductor-package bioconductor metabolomics gene genomics sequencing mass-spectrometry proteomics ontology feature-detection
Last synced: 10 months ago · JSON representation

Repository

A prototype backend to parse MassBank records into Spectra

Basic Info
Statistics
  • Stars: 3
  • Watchers: 5
  • Forks: 5
  • Open Issues: 8
  • Releases: 0
Topics
massbank spectra
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

Mass Spectrometry Data Backend for MassBank Files

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov license years in bioc Ranking by downloads build release build devel

The MsBackendMassbank package provides functionality to import and handle MS/MS spectrum data from Massbank files or to directly access a MassBank SQL database. The package defines the MsBackendMassbank and MsBackendMassbankSql backends which can be used to import and use MS2 spectrum data from mgf files respectively MySQL databases with the Spectra R package.

For more information see the package homepage.

Installation

The package can be installed with

r install.packages("BiocManager") BiocManager::install("MsBackendMassbank")

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.

Owner

  • Name: RforMassSpectrometry
  • Login: rformassspectrometry
  • Kind: organization
  • Email: maintainer@rformassspectrometry.org

R packages for mass spectrometry

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 4
  • Push event: 17
  • Pull request review event: 1
  • Pull request event: 6
  • Create event: 1
Last Year
  • Issues event: 2
  • Issue comment event: 4
  • Push event: 17
  • Pull request review event: 1
  • Pull request event: 6
  • Create event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 154
  • Total Committers: 5
  • Avg Commits per committer: 30.8
  • Development Distribution Score (DDS): 0.448
Past Year
  • Commits: 10
  • Committers: 2
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.2
Top Committers
Name Email Commits
jorainer j****r@g****m 85
Michael Witting m****g@h****e 48
J Wokaty j****y@s****u 10
Nitesh Turaga n****a@g****m 6
Michele Stravs s****m@i****h 5
Committer Domains (Top 20 + Academic)
imsb.biol.ethz.ch: 1 sph.cuny.edu: 1 helmholtz-muenchen.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 21
  • Total pull requests: 38
  • Average time to close issues: 2 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 3.1
  • Average comments per pull request: 0.37
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: about 4 hours
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • michaelwitting (9)
  • meowcat (3)
  • MonicaCalSan (3)
  • jorainer (2)
  • ksjewell (2)
  • Coayala (1)
  • eterlova (1)
Pull Request Authors
  • jorainer (22)
  • michaelwitting (15)
  • meowcat (1)
Top Labels
Issue Labels
enhancement (2) help wanted (1) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 24,927 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: MsBackendMassbank

Mass Spectrometry Data Backend for MassBank record Files

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 24,927 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 10.0%
Average: 13.8%
Stargazers count: 21.8%
Downloads: 37.1%
Maintainers (1)
maintainer@rformassspectrometry.org
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • Spectra >= 1.5.17 depends
  • BiocParallel * imports
  • DBI * imports
  • IRanges * imports
  • MsCoreUtils * imports
  • ProtGenerics * imports
  • S4Vectors * imports
  • methods * imports
  • utils * imports
  • BiocStyle >= 2.5.19 suggests
  • RSQLite * suggests
  • knitr >= 1.1.0 suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite