DaparToolshed
This is the development version of DaparToolshed; to use it, please install the devel version of Bioconductor.
Tools for the Differential Analysis of Proteins Abundance with R
Bioconductor version: Development (3.24)
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).
Author: Samuel Wieczorek [cre, aut]
, Thomas Burger [aut], Enora Fremy [ctb], Manon Gaudin [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek at cea.fr>
citation("DaparToolshed")):
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("DaparToolshed")
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("DaparToolshed")| Peptide workflow with DaparToolshed | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software |
| Version | 0.99.36 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | |
| URL | https://github.com/edyp-lab/DaparToolshed https://edyp-lab.github.io/DaparToolshed/ |
| Bug Reports | https://github.com/edyp-lab/DaparToolshed/issues |
See More
| 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 |
| 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 | DaparToolshed_0.99.36.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | DaparToolshed_0.99.36.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DaparToolshed |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DaparToolshed |
| Bioc Package Browser | https://code.bioconductor.org/browse/DaparToolshed/ |
| Package Short Url | https://bioconductor.org/packages/DaparToolshed/ |
| Package Downloads Report | Download Stats |