Table 9.
R packages with multifunctional workflows.
| Functionalities | Package | Reference | Repos |
|---|---|---|---|
| Convenience wrapper for pre-processing tools (xcms, CAMERA) and several statistical analyses. | MAIT | [302] | BioC |
| Pre-processing (xcms), replicate merging, noise, blank and missingness filtering, feature grouping, annotation of known compounds, isotopic labeling analysis, annotation from KEGG or HMDB, common biotransformations and probabilistic putative metabolite annotation using MetAssign. | mzMatch | [82,105] | GitHub |
| xcms and CAMERA-based workflow for non-targeted processing of LC-MS datasets. It includes pre-processing, peak picking, peak filtering, data normalisation and descriptive statistics calculation. | MStractor | GitHub | |
| Performs simultaneous raw data to mzXML conversion (MSConvert), peak picking, automatic PCA outlier detection and statistical analysis, visualisation and possible MS/MS target list determination during an MS1 metabolomic profiling experiment. | simExTargId | [303] | GitHub |
| Pre-processing of large LC-MS datasets. Performs automatic PCA with iterative automatic outlier removal and, clustering analysis and biomarker discovery. | MetMSLine | [304] | GitHub |
| Workflow for the systematic analysis of 1H NMR metabolomics dataset in quantitative genetics. Performs pre-processing, mQTL mapping, metabolites structural assignment and offers data visualisation tools. | mQTL.NMR | [144] | BioC |
| Workflow for pre-processing, quality control, annotation and statistical data analysis of LC-MS and GC-MS-based metabolomics data to be submitted to public repositories. | MetaDB | [305] | GitHub |
| Framework mainly built on several already published packages. It supports data processing form different analytical platforms (LC-MS, GC-MS, NMR, IR, UV-Vis). | specmine | [306] | GitHub |
| Common interface for several different MS-based data processing software. It covers various aspects, such as data preparation and data extraction, formula calculation, compound identification and reporting. | patRoon | GitHub | |
| Processing of high resolution of LC-MS data for environmental trend analysis. | enviMass | Zenodo | |
| Workflow for pre-processing of LC-HRMS data, suspect screening, screening for transformation products using combinatorial prediction, and interactive filtering based on ratios between sample groups. | RMassScreening | [307,308] | GitHub |
| Workflow to perform pre-processing, statistical analysis and metabolite identifications based on database search of detected spectra. | MetaboNexus | [309] | GitHub |
| shiny-based platform to extract differential features from LC-MS data, includes xcms-based feature detection, statistical analysis, prediction of molecular formulas, annotation of MS/MS spectra, MS/MS molecular networking and chemical compound database search. | METABOseek | GitHub | |
| shiny interface to Metabolomics packages and MetaboAnalyst scripts. | MetaboShiny | [310] | GitHub |
| Pre-processing and visualising LC-MS data, as well as statistical analyses, mainly based on univariate linear models. | amp | GitHub |