rMSI: an R package for MS imaging data handling and visualization

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Abstract

Summary:

R platform provides some packages that are useful to process mass spectrometry imaging (MSI) data; however, none of them provide an easy to use graphical user interface (GUI). Here, we introduce rMSI, an R package for MSI data analysis focused on providing an efficient way to manage MSI data together with a GUI integrated in R environment. MS data is loaded in rMSI custom format optimized to minimize the memory footprint yet maintaining a fast spectra access. The rMSI GUI is designed for simple and effective data exploration and visualization. Moreover, rMSI is designed to be integrated in the R environment through a library of functions that can be used to share MS data across others R packages. The release of rMSI for R environment establishes a novel and flexible platform for MSI data analysis, completely free and open-source.

Availability and Implementation:

The code, the documentation, a tutorial and example data are available open-source at: github.com/prafols/rMSI.

Contact:

jesus.brezmes@urv.cat

Supplementary information:

Supplementary data are available at Bioinformatics online.

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