Metabolomics and mass spec resources for Bioconductor incorporation

[mmulvahill]

I checked Biocondcutor and there were only 31 packages with the "metabolomics" search term. I removed some that were not obviously related. Attached is a list, but some of those may not be as relevant either - I don't have time now to look at each of them.

But if it helps, we are looking at data from LC/MS - which is related to GC/MS or other mass spectrometry (MS) based methods - but not related to NMR methods.

Packages I know better are 'xcms', which is widely used. The authors of "metabomxr" visited last year and we're in touch with them, they could be a good resource.

Other relevant packages from the Emory group that we work with: http://web1.sph.emory.edu/apLCMS/ https://sourceforge.net/projects/xmsanalyzer/

Package Name	Authors	Description
biosigner	Philippe Rinaudo Etienne Thevenot	Signature discovery from omics data
CAMERA	Steffen Neumann	Collection of annotation related methods for mass spectrometry data
cosmiq	David Fischer Christian Panse	cosmiq - COmbining Single Masses Into Quantities
IPO	Thomas Riebenbauer	Automated Optimization of XCMS Data Processing parameters
MAIT	Francesc Fernandez-Albert	Statistical Analysis of Metabolomic Data
Metab	Raphael Aggio	Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
metabomxtr	Michael Nodzenski	A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
metaMS	Ron Wehrens	MS-based metabolomics annotation pipeline
MetCirc	Thomas Naake	Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
MWASTools	Andrea Rodriguez-Martinez Rafael Ayala	MWASTools: an integrated pipeline to perform metabolome-wide association studies
mzR	Bernd Fischer Steffen Neumann Laurent Gatto Qiang Kou	parser for netCDF mzXML mzData and mzML and mzIdentML files (mass spectrometry data)
OmicsMarkeR	Charles E. Determan Jr.	Classification and Feature Selection for 'Omics' Datasets
PAPi	Raphael Aggio	Predict metabolic pathway activity based on metabolomics data
pathview	Weijun Luo	a tool set for pathway based data integration and visualization
Rdisop	Steffen Neumann	Decomposition of Isotopic Patterns
RMassBank	RMassBank at Eawag	Workflow to process tandem MS files and build MassBank records
ropls	Etienne A. Thevenot	PCA PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
SIMAT	Mo R. Nezami Ranjbar	GC-SIM-MS data processing and alaysis tool
statTarget	Hemi Luan	Statistical Analysis of Metabolite Profile
xcms	Steffen Neumann	LC/MS and GC/MS Data Analysis
yamss	Leslie Myint	Tools for high-throughput metabolomics

[mmulvahill]

The xcms package (actually xcms3 now) has promising ideas for incorporation with bioconductor.

• Make use and extend classes defined in the MSnbase package.
• Implement class versioning (Biobase’s Versioned class).
• Use BiocParallel for parallel processing.

from the xcmsPreprocess vignette -- what are these file formats:

AIA/ANDI format NetCDF, mzXML, and mzData files Should know this before fixing readdata()...

[mmulvahill]

Next question to get answered — what in-data format do we want? Do any of these MSnbase formats apply?

[mmulvahill]

We agreed to submit to CRAN and if possible rOpenSci instead of Bioconductor -- none of our statisticians use enough of the Bioconductor infrastructure to make it worth the effort to add support for the necessary S4 classes.