Package: TraianProt
Title: TraianProt: a user-friendly R package for wide format proteomics
        data downstream analysis
Version: 0.99.16
Authors@R: 
    person("Samuel", "de la Camara Fuentes", , "sdelacam@ucm.es", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6718-5896"))
Description: A proteomics data analysis platform that enables the analysis
    of both label-free and labeled data from Data-Dependent or
    Data-Independent Acquisition mass spectrometry mode, supporting
    MaxQuant, MSFragger, DIA-NN, ProteoScape, and Proteome Discoverer
    output formats. TraianProt provides a comprehensive suite of stepwise
    downstream analysis modules, which includes data filtering,
    normalization procedures, and missing value imputation strategies. The
    platform also incorporates robust statistical frameworks for
    differential expression testing, with peptide-spectrum match level
    correction, thereby enhancing the reliability of biological
    interpretations.
License: GPL (>= 3)
biocViews: Software, Proteomics, MassSpectrometry, DataImport,
        Normalization, DifferentialExpression, GO
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://github.com/SamueldelaCamaraFuentes/TraianProt
BugReports: https://github.com/SamueldelaCamaraFuentes/TraianProt/issues
Imports: dplyr, ggplot2, ggrepel, ggExtra, VennDiagram, pheatmap, VIM,
        grid, wrProteo, wrMisc, gplots, gprofiler2, writexl, readxl,
        data.table, igraph, stringr, limma, methods, grDevices,
        graphics, stats, matrixStats, tidyr, tibble, DEqMS, plotly,
        DOSE, enrichplot, STRINGdb, Rtsne, shiny, shinyWidgets,
        shinydashboard, DT, rmarkdown, clusterProfiler,
        SummarizedExperiment
Suggests: knitr, BiocStyle, testthat
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TraianProt
git_branch: devel
git_last_commit: ee5dcc0
git_last_commit_date: 2026-07-16
Repository: Bioconductor 3.24
Date/Publication: 2026-07-20
NeedsCompilation: no
Packaged: 2026-07-20 23:00:25 UTC; biocbuild
Author: Samuel de la Camara Fuentes [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6718-5896>)
Maintainer: Samuel de la Camara Fuentes <sdelacam@ucm.es>
Built: R 4.6.1; ; 2026-07-21 05:58:10 UTC; unix
