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DaparToolshed

Tools for the Differential Analysis of Proteins Abundance with R

Bioconductor version: 3.24 · Package version: 0.99.38

The package DaparToolshed is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. It is an update of our previous package DAPAR and contains more functions to analyze the data and uses MultAssayExperiment and SummarizedExperiment data structures. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DaparToolshed")

Details

MaintainerSamuel Wieczorek <samuel.wieczorek@cea.fr>
AuthorSamuel Wieczorek [cre, aut] (ORCID: <https://orcid.org/0000-0002-5016-1203>), Thomas Burger [aut], Enora Fremy [ctb], Manon Gaudin [ctb]
LicenseArtistic-2.0
URLhttps://github.com/edyp-lab/DaparToolshed, https://edyp-lab.github.io/DaparToolshed/
Bug Reportshttps://github.com/edyp-lab/DaparToolshed/issues
Downloads rank56
Source branchdevel
biocViewsDataImport, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageDaparToolshed_0.99.38.tar.gz
Windows binary (x86_64)DaparToolshed_0.99.38.zip
macOS binary (arm64)DaparToolshed_0.99.38.tgz
macOS binary (x86_64)DaparToolshed_0.99.38.tgz
Dependencies

Depends: R (>= 4.5.0)

Imports: BiocGenerics, matrixStats, S4Vectors, SummarizedExperiment, openxlsx, QFeatures (>= 1.16), methods, MsCoreUtils, AnnotationFilter, RColorBrewer, plotly, stats, utils, tibble, Matrix, stringr, graph, igraph, preprocessCore, dplyr

Suggests: BiocManager, visNetwork, htmlwidgets, rhandsontable, shinyalert, shinyjs, sos, knitr, shinyBS, MultiAssayExperiment, PSMatch, lme4, DT, shinyWidgets, vsn, cp4p, limma, imp4p (>= 0.9), impute, apcluster, diptest, cluster, rmarkdown, BiocStyle, testthat, FactoMineR, factoextra, colourpicker, readxl, grDevices, forcats, multcomp, purrr, gplots, tidyr, Pirat, shinyjqui