Package: bppg
Title: Bipartite peptide-protein graphs
Version: 0.99.1
Date: 2026-08-12
Authors@R: c(
    person("Karin", "Schork", , "karin.schork@rub.de", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-3756-4347")),
    person("Julika", "Wenzel", , "julika.wenzel@rub.de", role = c("aut"),
           comment = c(ORCID = "0009-0004-1468-5984")),
    person("Katharina", "Neuhaus", , "katharina.neuhaus@rub.de", role = c("aut")), 
    person("Martin", "Eisenacher", , "martin.eisenacher@rub.de", role = c("aut", "fnd"), 
    comment = c(ORCID = "0000-0003-2687-7444")))
Description: This package contains functionality to create and
        characterize bipartite graphs that model the relationship
        between peptides and proteins in bottom-up proteomics. With
        these graphs, protein ratios (fold change between two sample
        groups) are calculated from the respective measured peptide
        ratios. The main aim is to make use of quantitative information
        contained in shared peptides and making it possible to quantify
        proteins without shared peptides. Further, the package offers
        general analysis of peptide and protein relationships using
        bipartite graphs and visualization for these graphs.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
biocViews: Proteomics, GraphAndNetwork, MassSpectrometry,
        MultipleComparison, Visualization
Imports: checkmate, ggplot2, ggraph, limma, openxlsx, pbapply,
        robustbase, Rsolnp, stringr, SummarizedExperiment, vsn
Suggests: covr, rmarkdown, testthat (>= 3.0.0),
        tidySummarizedExperiment, seqinr, BiocStyle, knitr, pak,
        RefManageR, sessioninfo, batchtools
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: R (>= 3.5.0), igraph (>= 2.0.0)
Config/roxygen2/version: 8.1.0
URL: https://github.com/mpc-bioinformatics/bppg
BugReports: https://github.com/mpc-bioinformatics/bppg/issues
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libglpk-dev
        libicu-dev libxml2-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-12 12:14:48 UTC
RemoteUrl: https://github.com/BiocStaging/bppg
RemoteRef: HEAD
RemoteSha: e3f64d0f75108a1114b1ab00d2e1b34c0b657f81
NeedsCompilation: no
Packaged: 2026-10-11 10:05:25 UTC; root
Author: Karin Schork [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3756-4347>),
  Julika Wenzel [aut] (ORCID: <https://orcid.org/0009-0004-1468-5984>),
  Katharina Neuhaus [aut],
  Martin Eisenacher [aut, fnd] (ORCID:
    <https://orcid.org/0000-0003-2687-7444>)
Maintainer: Karin Schork <karin.schork@rub.de>