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

• Published in: Bioinformatics (Oxford, England) Vol. 33; no. 15; pp. 2427 - 2428
• Main Authors: Ràfols, Pere, Torres, Sònia, Ramírez, Noelia, Del Castillo, Esteban, Yanes, Oscar, Brezmes, Jesús, Correig, Xavier
• Format: Journal Article
• Language: English
• Published: England 01.08.2017
• Subjects: Animals; Brain - metabolism; Image Processing, Computer-Assisted - methods; Mass Spectrometry - methods; Mice; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btx182

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. The code, the documentation, a tutorial and example data are available open-source at: github.com/prafols/rMSI. jesus.brezmes@urv.cat. Supplementary data are available at Bioinformatics online.