Introduction | Importing the source data | Building the model sequence | Normalising synonyms | Translation and merging (MMS Step 1) | Attribute retrieval (MMS Step 2) | Manual curation (MMS Step 3) | The complete sequence | What the harmonised tables look like | Comparison against the published result | Characterising the mismatch | Learnings and Benefits of MetMashR | References | Session Info

Getting Started | Introduction | Input data | Importing the annotations | Importing Compound Discoverer annotations | Importing LipidSearch annotations | Exploratory analysis of annotation sources | Combining Annotation Sources | Adding identifiers | Improving ID coverage | Comparison with the true mixtures | Importing the standard mixture tables | Identifiers for the standards | Comparison of standards and annotations | Session Info

Getting Started | Introduction | Importing the MTox700+ database | Exploring the chemical space | Exploring the biological space | Importing PathBank | Comparing PathBank and MTox700+ | Combining MTox700+ with PathBank | Combining records | Session Info

Introduction | Getting Started | Example study | Annotation Sources | Adding new annotation sources | The class definition | The calling function | The import method | Using the new source | Adding annotation workflow steps | Empty column removal | Suffix removal | Metabolite mashing | Summary | Session Info

Introduction | Statistics in R using Class Templates (struct) | Getting Started | Annotation Sources | Annotation Tables | Annotation Databases | Cached databases | Annotation Mashing | Importing sources | Filtering / Cleaning | LCMS peak matching | REST APIs | Dictionaries | Combining Records | Session Info

Introduction | Getting started | struct helper functions | Creating a new struct object | Changing the default methods | Changing the default show output | Class-based templates and struct objects | DatasetExperiment objects | model objects | using the model template | model_seq objects | iterator objects | metric objects | chart objects | entity and enum objects | Ontology | Session Info

Introduction | Getting started | Case Studies | Tutorials | Session Info

Introduction | Installation | Querying the database | Choosing a study | Workflow | Session Info

Introduction | Installation | Running a query | Special cases | input_item "ignored" | output_item "compound_exact", "protein_exact" and "gene_exact" | output_item "protein_partial" and "gene_partial" | output_item "SummarizedExperiment" and "DatasetExperiment" | output_item "MultiAssayExperiment" | output_item "untarg_SummarizedExperiment" and "untarg_DatasetExperiment" | S4 classes | Contexts | Input / Output Items | Session Info

Introduction | Installation | Data formats | Example dataset, MTBLS79 | Filtering a dataset | Processing history | Data normalisation | Missing value imputation | Data scaling | Data integrity check and endomorphisms | Session information | References

Introduction | Installation | Dataset | Exploratory data analysis | Correlation between signal intensity and injection order of QC samples | Using regression to estimate signal trends and variability across QC sample | Example of signal drift and batch effect correction for a single feature | Signal drift and batch effect correction using smoothed spline fitting | Session information | References

Introduction | Installation | Dataset | Missing values | Applying signal drift and batch effect correction | Visual comparison of the results | Session information | References