Data

Tools

Indexes

Applications

Experiments

Open Source Science

msqrob2

Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure

https://github.com/statomics/msqrob2

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 11 committers (9.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords from Contributors

bioconductor bioconductor-package software single-cell proteomics mass-spectrometry proteomexchange ontology metabolomics gene
Last synced: 10 months ago · JSON representation

Repository

Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure

Basic Info
  • Host: GitHub
  • Owner: statOmics
  • Language: R
  • Default Branch: master
  • Size: 175 MB
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 12
  • Open Issues: 26
  • Releases: 0
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

R-CMD-check-bioc Codecov test coverage <!-- badges: end -->

R package: msqrob2

Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure

The msqrob2 package ports and modernises the method presented in MSqRob and MSqRobSum to use the QFeatures class infrastructure.

Installation

To install the current version of msqrob2, run.

if(!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("statOmics/msqrob2")

The dependencies of the package are listed in the DESCRIPTION file of the package.

Issues and bug reports

Please use https://github.com/statOmics/msqrob2/issues to submit issues, bug reports, and comments.

Usage

See vignettes on msqrob2Examples

Owner

  • Name: statOmics
  • Login: statOmics
  • Kind: organization

GitHub Events

Total
  • Issues event: 1
  • Watch event: 3
  • Issue comment event: 5
  • Push event: 8
  • Pull request review event: 8
  • Pull request review comment event: 4
  • Pull request event: 3
  • Fork event: 2
  • Create event: 1
Last Year
  • Issues event: 1
  • Watch event: 3
  • Issue comment event: 5
  • Push event: 8
  • Pull request review event: 8
  • Pull request review comment event: 4
  • Pull request event: 3
  • Fork event: 2
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 144
  • Total Committers: 11
  • Avg Commits per committer: 13.091
  • Development Distribution Score (DDS): 0.542
Past Year
  • Commits: 15
  • Committers: 3
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
statOmics l****t@u****e 66
Milan Malfait m****4@g****m 20
Oliver M. Crook o****k@g****m 19
StijnVandenbulcke v****n@g****m 15
Nitesh Turaga n****a@g****m 6
Lieven Clement l****t@g****m 5
Laurent Gatto l****o@u****e 5
StijnVandenbulcke 5****e 4
J Wokaty j****y@s****u 2
cvanderaa 4****a 1
Laurent Gatto l****o@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 uclouvain.be: 1 ugent.be: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 37
  • Total pull requests: 27
  • Average time to close issues: 22 days
  • Average time to close pull requests: about 1 month
  • Total issue authors: 19
  • Total pull request authors: 6
  • Average comments per issue: 2.41
  • Average comments per pull request: 0.81
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 7
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 0.6
  • Average comments per pull request: 1.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ococrook (8)
  • statOmics (5)
  • lgatto (4)
  • PB-Shinde (2)
  • cvanderaa (2)
  • EmilieCarneiro (2)
  • JobbeG (2)
  • Aintzane99 (1)
  • Douerww (1)
  • Mengbo-Li (1)
  • milanmlft (1)
  • mbonhomme (1)
  • DrSAUD (1)
  • Apirog9 (1)
  • yafeng (1)
Pull Request Authors
  • StijnVandenbulcke (14)
  • ococrook (8)
  • milanmlft (5)
  • cvanderaa (3)
  • leopoldguyot (2)
  • lgatto (1)
Top Labels
Issue Labels
duplicate (1) documentation (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 11,052 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: msqrob2

Robust statistical inference for quantitative LC-MS proteomics

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 11,052 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 6.8%
Average: 21.3%
Stargazers count: 21.8%
Downloads: 77.9%
Maintainers (1)
lieven.clement@ugent.be
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • QFeatures >= 1.1.2 depends
  • R >= 4.1 depends
  • BiocParallel * imports
  • MASS * imports
  • Matrix * imports
  • SummarizedExperiment * imports
  • codetools * imports
  • limma * imports
  • lme4 * imports
  • methods * imports
  • purrr * imports
  • stats * imports
  • BiocStyle * suggests
  • MSnbase * suggests
  • MsCoreUtils * suggests
  • RefManageR * suggests
  • gridExtra * suggests
  • knitr * suggests
  • matrixStats * suggests
  • msdata * suggests
  • multcomp * suggests
  • plotly * suggests
  • rmarkdown * suggests
  • sessioninfo * suggests
  • testthat * suggests
  • tidyverse * suggests
.github/workflows/check-bioc.yml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • grimbough/bioc-actions/build-install-check v1 composite
  • grimbough/bioc-actions/run-BiocCheck v1 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-pandoc 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 v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite