TraianProt
This is the development version of TraianProt; to use it, please install the devel version of Bioconductor.
TraianProt: a user-friendly R package for wide format proteomics data downstream analysis
Bioconductor version: 3.24 · Package version: 0.99.17
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.
Author: Samuel de la Camara Fuentes [aut, cre] 
Maintainer: Samuel de la Camara Fuentes <sdelacam at ucm.es>
Citation
From within R, enter citation("TraianProt"):
Samuel de la Camara Fuentes. TraianProt: TraianProt: a user-friendly R package for wide format proteomics data downstream analysis. doi:10.18129/B9.bioc.TraianProt, R package version 0.99.17, https://bioconductor.org/packages/TraianProt.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TraianProt")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.17 |
| License | GPL (>= 3) |
| URL | https://github.com/SamueldelaCamaraFuentes/TraianProt |
| Bug Reports | https://github.com/SamueldelaCamaraFuentes/TraianProt/issues |
| Last updated | 2026-07-30 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2401 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DifferentialExpression, GO, MassSpectrometry, Normalization, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/TraianProt/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TraianProt")| TraianProt: A Comprehensive package for Proteomics Data Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | TraianProt_0.99.17.tar.gz |
| Windows binary (x86_64) | TraianProt_0.99.17.zip |
| macOS binary (arm64) | TraianProt_0.99.17.tgz |
| macOS binary (x86_64) | TraianProt_0.99.17.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TraianProt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TraianProt |
| Package Downloads Report | Download Stats |
Dependencies
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