rMSIproc: an R package for mass spectrometry imaging data processing.
Bioinformatics 2020;
36:3618-3619. [PMID:
32108859 DOI:
10.1093/bioinformatics/btaa142]
[Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/22/2020] [Accepted: 02/25/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY
Mass spectrometry imaging (MSI) can reveal biochemical information directly from a tissue section. MSI generates a large quantity of complex spectral data which is still challenging to translate into relevant biochemical information. Here, we present rMSIproc, an open-source R package that implements a full data processing workflow for MSI experiments performed using TOF or FT-based mass spectrometers. The package provides a novel strategy for spectral alignment and recalibration, which allows to process multiple datasets simultaneously. This enables to perform a confident statistical analysis with multiple datasets from one or several experiments. rMSIproc is designed to work with files larger than the computer memory capacity and the algorithms are implemented using a multi-threading strategy. rMSIproc is a powerful tool able to take full advantage of modern computer systems to completely develop the whole MSI potential.
AVAILABILITY AND IMPLEMENTATION
rMSIproc is freely available at https://github.com/prafols/rMSIproc.
CONTACT
pere.rafols@urv.cat.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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