Packages
This page lists some core packages from RforMassSpectrometry. For a full listing of currently available package see the project’s R universe page.
Installation and use
Execute
BiocManager::install("RforMassSpectrometry/RforMassSpectrometry") to
install all the RforMassSpectrometry packages.
Load the core packages with library("RforMassSpectrometry").
Packages
RforMassSpectrometry
RforMassSpectrometry is a meta-package that is used to manage the R for Mass Spectrometry suite and core package versions in a coherent way. Users will rely on this package to install and manage the other packages. Learn more ...
MsExperiment
The MsExperiment package provides the infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry experiment. It relies on the other RforMassSpectrometry core packages for the data crunching. Learn more ...
Spectra
The Spectra package provides base classes and processing methods for raw mass spectrometry data. It is designed with efficiency, both in terms of memory footprint and processing time in mind, and can manage data in different types of formats. Learn more ...
QFeatures
The QFeatures package offers the infrastructure to manage and process quantitative features for high-throughput mass spectrometry assays, including proteomics and metabolomics experiments. Learn more ...
PSMatch
The PSMatch package allows to read, process and analyse peptide-spectrum matches. Learn more ...
Chromatograms
The Chromatograms package provides base classes and processing methods for chromatographic data. It is designed with efficiency, both in terms of memory footprint and processing time in mind, and can manage data in different types of formats. Learn more ...
MsCoreUtils
The MsCoreUtils package defines low-level functions for mass spectrometry data processing and is independent of any high-level data structures. Learn more ...
MetaboCoreUtils
The MetaboCoreUtils package defines low-level functions for common operations in metabolomics and is independent of any high-level data structures. Learn more ...
Get started
Each package comes with ample documentation, directly available on-line on the respective package webpages. All vignettes are also available here. The R for Mass Spectrometry book is also a good way to learn how to use some of the most important packages of the project.
Get help
For questions about specific software or their usage, please refer to the software’s github issue page, or use the Bioconductor support site.