Package for Peak Picking and ANnoTation of High resolution Experiments in R, implemented in
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:
onefile at a time
parallel, store results in a
peakPantheR can process LC/MS data files in NetCDF, mzML/mzXML and mzData format as data import is achieved using Bioconductor’s
To install peakPantheR:
To install the development version from GitHub:
Both real time and parallel compound integration require a common set of information:
m/zwindow) for each compound.
An overview of the package and detailed information on usage are available in the following vignettes:
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.
peakPantheR is licensed under the GPLv3
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 (2020)
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