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R Interface to the ProteomeXchange Repository

Thre rpx package is a simple programmatic interface to proteomics data available in the ProteomeXchange repository. It uses a ProteomeXchange identifier such as PXD000001 to find and download files associated with that project. The official Bioconductor is here. The GitHub page allows to browse the documentation and the vignette.

Installation

To install the version matching your local R installation from the Bioconductor repository:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("rpx")

And to install the very latest version from GitHub:

BiocManager::install("lgatto/rpx")

For a similar python-based software, see ppx by Will Fondrie.