Repository files navigation

Package forPeak Picking and ANnoTation of High resolution Experiments in R, implemented inR andShiny

peakPantheR is an R/Bioconductor package that implements functions to detect, integrate and report pre-defined features in MS files (e.g. compounds, fragments, adducts, …). It is designed for:

• Real time feature detection and integration (seeReal Time Annotation)
  • processmultiple compounds inone file at a time
• Post-acquisition feature detection, integration and reporting (seeParallel Annotation)
  • processmultiple compounds inmultiple files inparallel, store results in asingle object

peakPantheR can process LC/MS data files inNetCDF,mzML/mzXML andmzData format as data import is achieved using Bioconductor’smzR package.

The reference versions ofpeakPantheR is available on the corresponding Bioconductor page (release ordev version).

Active development and issue tracking take place on thegithub page, while an overview of the package, vignettes and documentation are available on thesupporting website.

To installpeakPantheR:

install.packages("BiocManager")BiocManager::install("peakPantheR")

To install the development version from GitHub:

BiocManager::install("phenomecentre/peakPantheR")

Both real time and parallel compound integration require a common set of information:

• Path(s) tonetCDF /mzML MS file(s)
• An expected region of interest (RT /m/z window) for each compound.

An overview of the package and detailed information on usage are available in the following vignettes:

• Getting Started with peakPantheR
• Real Time Annotation
• Parallel Annotation
• Graphical user interface use

Besides the vignettes, more tutorials are available via github:

• Targeted integration of metabolites from 3 LC-MS profiling dataset using peakPantheR: Application of peakpPantheR to extract features from 3 LC-MS assays from a human urine metabolic profiling study on cognitive decline and dementia.
• Quality-Control of peakPantheR extracted using the nPYc-Toolbox: Tutorial on how to use the nPYC-Toolbox to perform QC on peakPanther extracted datasets.

Suggestions and contributions topeakPantheR are welcome, for more information please first refer to thecontribution guide and code of conduct, or get in touch by opening aGithub issue.

peakPantheR is licensed under theGPLv3

As a summary, the GPLv3 license requires attribution, inclusion of copyright and license information, disclosure of source code and changes. Derivative work must be available under the same terms.

© National Phenome Centre (2025)