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MsExperiment

Managing and Processing Mass Spectrometry Experiments

https://github.com/rformassspectrometry/msexperiment

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 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords from Contributors

bioconductor mass-spectrometry metabolomics proteomics bioconductor-package feature-detection peak-detection annotation proteomexchange single-cell
Last synced: 10 months ago · JSON representation

Repository

Managing and Processing Mass Spectrometry Experiments

Basic Info
Statistics
  • Stars: 5
  • Watchers: 4
  • Forks: 4
  • Open Issues: 4
  • Releases: 0
Created about 7 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

Managing mass spectrometry experiments

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 MsExperiment package provides the MsExperiment class that can be used to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry experiment. This includes

  • experimental design
  • data files
  • raw data: spectra and chromatograms
  • proteomics identification results and protein database
  • quantitative features

The respective data handling functionality is handled by dedicated packages such as Spectra for spectra data, QFeatures for quantitative features, Biostrings for fasta files, ...

See the package homepage for more information.

This package is part of the RforMassSpectrometry initiative: https://www.rformassspectrometry.org/

Installation

The package can be installed with

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

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: 1
  • Issue comment event: 3
  • Push event: 7
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 1
  • Issue comment event: 3
  • Push event: 7
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 105
  • Total Committers: 6
  • Avg Commits per committer: 17.5
  • Development Distribution Score (DDS): 0.552
Past Year
  • Commits: 19
  • Committers: 5
  • Avg Commits per committer: 3.8
  • Development Distribution Score (DDS): 0.316
Top Committers
Name Email Commits
jorainer j****r@g****m 47
lgatto l****o@g****m 37
Laurent Gatto l****o@u****e 16
Johannes Rainer 5****r 2
J Wokaty j****y@s****u 2
Jan Stanstrup s****p@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 uclouvain.be: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 17
  • Total pull requests: 28
  • Average time to close issues: 8 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.93
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 months
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 2.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jorainer (11)
  • lgatto (3)
  • philouail (2)
  • sneumann (1)
Pull Request Authors
  • lgatto (15)
  • jorainer (12)
  • stanstrup (1)
  • TuomasBorman (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 47,529 total
  • Total dependent packages: 2
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: MsExperiment

Infrastructure for Mass Spectrometry Experiments

  • Versions: 6
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 47,529 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 14.4%
Stargazers count: 19.5%
Average: 24.2%
Downloads: 87.1%
Maintainers (1)
laurent.gatto@uclouvain.be
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • ProtGenerics >= 1.9.1 depends
  • R >= 4.2 depends
  • IRanges * imports
  • QFeatures * imports
  • S4Vectors * imports
  • Spectra * imports
  • SummarizedExperiment * imports
  • methods * imports
  • BiocStyle >= 2.5.19 suggests
  • knitr >= 1.1.0 suggests
  • msdata * suggests
  • mzR * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • rpx * 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