Package: PepSetTest
Title: Peptide Set Test
Version: 1.7.0
Authors@R: 
    person("Junmin", "Wang", , "jmwang.bio@gmail.com", role = c("aut", "cre"))
Description: Peptide Set Test (PepSetTest) is a peptide-centric
        strategy to infer differentially expressed proteins in LC-MS/MS
        proteomics data. This test detects coordinated changes in the
        expression of peptides originating from the same protein and
        compares these changes against the rest of the peptidome.
        Compared to traditional aggregation-based approaches, the
        peptide set test demonstrates improved statistical power, yet
        controlling the Type I error rate correctly in most cases. This
        test can be valuable for discovering novel biomarkers and
        prioritizing drug targets, especially when the direct
        application of statistical analysis to protein data fails to
        provide substantial insights.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: dplyr, limma, lme4, MASS, matrixStats, reshape2, stats,
        tibble, SummarizedExperiment, methods
Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr
biocViews: DifferentialExpression, Regression, Proteomics,
        MassSpectrometry
VignetteBuilder: knitr
URL: https://github.com/JmWangBio/PepSetTest
BugReports: https://github.com/JmWangBio/PepSetTest/issues
Config/pak/sysreqs: cmake make libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:03:21 UTC
RemoteUrl: https://github.com/bioc/PepSetTest
RemoteRef: HEAD
RemoteSha: 116c76e6daee4e889a7af7b52ca7f2b96df7b75a
NeedsCompilation: no
Packaged: 2026-07-04 10:50:09 UTC; root
Author: Junmin Wang [aut, cre]
Maintainer: Junmin Wang <jmwang.bio@gmail.com>
Depends: R (>= 4.1.0)