AlpsNMR is an R package that can load Bruker and JDX samples as well as preprocess them.

It includes functions for region exclusion, normalization, peak detection & integration and outlier detection among others. See the package vignette for details.

Installation

if (!"BiocManager" %in% rownames(installed.packages()))  
    install.packages("BiocManager")
BiocManager::install("AlpsNMR")

Alternative installation

AlpsNMR can be installed with the devtools package. For this is needed Rtools and note that it uses packages from CRAN, from BioConductor and from git repositories:

If you already have Rtools, follow this to install AlspNMR:

if (!"BiocManager" %in% rownames(installed.packages()))  
    install.packages("BiocManager")  
BiocManager::install(c("MassSpecWavelet", "impute"), update = FALSE)  
if (!"devtools" %in% rownames(installed.packages()))  
    install.packages("devtools")  
devtools::install_github("sipss/AlpsNMR")

If you need install Rtools: Follow steps of Rtools website [Rtools web]

Don’t forget the additional step, Putting Rtools on the PATH.

Install AlpsNMR:

if (!"BiocManager" %in% rownames(installed.packages()))  
    install.packages("BiocManager")  
BiocManager::install(c("MassSpecWavelet", "impute"), update = FALSE)  
if (!"devtools" %in% rownames(installed.packages()))  
    install.packages("devtools")  
devtools::install_github("sipss/AlpsNMR")

Quick start

Checkout the Introduction to AlpsNMR vignette that shows how to import data and preprocess it using AlpsNMR. See our publication for further details.

See also the tutorial with a real dataset from beginning to end, including all the steps of untargeted metabolomics analysis.