rpx

This is the development version of rpx; for the stable release version, see rpx.

R Interface to the ProteomeXchange Repository

Bioconductor version: Development (3.24)

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

Author: Laurent Gatto

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

Citation (from within R, enter citation("rpx")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

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("rpx")

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("rpx")

An R interface to the ProteomeXchange repository	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, ImmunoOncology, MassSpectrometry, Proteomics, Software, ThirdPartyClient
Version	2.21.0
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	GPL-2
Depends	R (>= 3.5.0), methods
Imports	BiocFileCache, jsonlite, xml2, RCurl, curl, utils
System Requirements
URL	https://github.com/lgatto/rpx
Bug Reports	https://github.com/lgatto/rpx/issues

Suggests	Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	MsExperiment, MSnbase, PSMatch, RforProteomics
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rpx_2.21.0.tar.gz
Windows Binary (x86_64)	rpx_2.21.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	rpx_2.21.0.tgz
macOS Binary (sonoma-arm64)	rpx_2.21.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rpx
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rpx
Bioc Package Browser	https://code.bioconductor.org/browse/rpx/
Package Short Url	https://bioconductor.org/packages/rpx/
Package Downloads Report	Download Stats