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: Development (3.24)
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("TraianProt")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("TraianProt")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TraianProt")| TraianProt | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DifferentialExpression, GO, MassSpectrometry, Normalization, Proteomics, Software |
| Version | 0.99.16 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | |
| 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 |
| System Requirements | |
| URL | https://github.com/SamueldelaCamaraFuentes/TraianProt |
| Bug Reports | https://github.com/SamueldelaCamaraFuentes/TraianProt/issues |
See More
| Suggests | knitr, BiocStyle, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TraianProt_0.99.16.tar.gz |
| Windows Binary (x86_64) | TraianProt_0.99.16.zip |
| macOS Binary (big-sur-x86_64) | TraianProt_0.99.16.tgz |
| macOS Binary (sonoma-arm64) | TraianProt_0.99.16.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TraianProt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TraianProt |
| Bioc Package Browser | https://code.bioconductor.org/browse/TraianProt/ |
| Package Short Url | https://bioconductor.org/packages/TraianProt/ |
| Package Downloads Report | Download Stats |