The MetaRbolomics book
Preface
How to …
This book in other formats
1
Introduction
1.1
Metabolomics data processing and analysis
1.2
The R package landscape
1.3
Dependences and connectivity of metabolomics packages
2
R-packages for metabolomics
2.1
Mass spectrometry data handling and (pre-)processing
2.1.1
Profile mode and centroided data
2.1.2
Direct infusion mass spectrometry data
2.1.3
Hyphenated MS and non-targeted data
2.1.4
Targeted data and alternative representations of data
2.1.5
Additional dimensionality
2.1.6
Structuring data and metadata
2.1.7
Ion species grouping and annotation
2.2
Metabolite identification with MS/MS data
2.2.1
MS/MS data handling, spectral matching and clustering
2.2.2
Reading of spectral databases
2.3
NMR data handling and (pre-)processing
2.4
UV data handling and (pre-)processing
2.5
Statistical analysis of metabolomics data
2.6
Handling of molecule structures and chemical structure databases
2.7
Network analysis and biochemical pathways
2.7.1
Network infrastructure and analysis
2.7.2
Metabolite annotation
2.7.3
Generation of metabolic networks
2.7.4
Pathway analysis
2.7.5
Pathway resources and interfaces
2.8
Multifunctional workflows
2.9
User interfaces and workflow management systems
2.10
Metabolomics data sets
3
Conclusions
References
Appendices
Appendix 1: The MSP File Format and package support
Appendix 2: metaRbolomics dependencies network
Libraries and settings
Read package names from our table
Get reverse dependencies
Building dependency network
Save network plot
Notes
Published with bookdown
The MetaRbolomics book
Appendices