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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-16 13:27:26 UTC
RemoteUrl: https://github.com/bioc/TraianProt
RemoteRef: HEAD
RemoteSha: ee5dcc08bcf0976549253d10d63ac4602392a46f
NeedsCompilation: no
Packaged: 2026-07-22 10:51:21 UTC; root
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>