Package: PRONE
Type: Package
Title: The PROteomics Normalization Evaluator
Version: 1.4.0
Authors@R: c(person("Lis", "Arend", email = "lis.arend@tum.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7990-8385")))
Description: High-throughput omics data are often affected by
        systematic biases introduced throughout all the steps of a
        clinical study, from sample collection to quantification.
        Normalization methods aim to adjust for these biases to make
        the actual biological signal more prominent. However, selecting
        an appropriate normalization method is challenging due to the
        wide range of available approaches. Therefore, a comparative
        evaluation of unnormalized and normalized data is essential in
        identifying an appropriate normalization strategy for a
        specific data set. This R package provides different functions
        for preprocessing, normalizing, and evaluating different
        normalization approaches. Furthermore, normalization methods
        can be evaluated on downstream steps, such as differential
        expression analysis and statistical enrichment analysis.
        Spike-in data sets with known ground truth and real-world data
        sets of biological experiments acquired by either tandem mass
        tag (TMT) or label-free quantification (LFQ) can be analyzed.
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0), SummarizedExperiment
Imports: dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors,
        ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS,
        edgeR, matrixStats, preprocessCore, stats, gtools, methods,
        ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2,
        plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2,
        POMA, ggtext, scales, DEqMS, vegan
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT
BugReports: https://github.com/daisybio/PRONE/issues
URL: https://github.com/daisybio/PRONE
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Proteomics, Preprocessing, Normalization,
        DifferentialExpression, Visualization
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev libglu1-mesa-dev libgmp3-dev make texlive
        libicu-dev libjpeg-dev libpng-dev libxml2-dev libmpfr-dev
        libnetcdf-dev libgl1-mesa-dev libssl-dev perl zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:32:38 UTC
RemoteUrl: https://github.com/bioc/PRONE
RemoteRef: RELEASE_3_22
RemoteSha: 2b31a49c7e669b4d5b67964fb27b9c28ddb76c5a
NeedsCompilation: no
Packaged: 2026-01-24 07:33:28 UTC; root
Author: Lis Arend [aut, cre] (ORCID: <https://orcid.org/0000-0001-7990-8385>)
Maintainer: Lis Arend <lis.arend@tum.de>
Built: R 4.5.2; ; 2026-01-24 07:36:06 UTC; windows
