README.md

In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

AlpsLCMS

The goal of AlpsLCMS is to offer a data analysis preprocessing pipeline for LC/MS metabolomic samples.

Installation

AlpsLCMS 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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")

BiocManager::install(c("xcms", "mzR"))
BiocManager::install(c("CAMERA"))
BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
BiocManager::install(c(faahKO"))
remotes::install_github("cbroeckl/RAMClustR")
devtools::install_git("https://gitlab.com/CarlBrunius/StatTools.git")

devtools::install_github("sipss/AlpsLCMS")

 Quick start ========================

Checkout the Introduction to AlpsLCMS vignette that shows how to import data and preprocess it using AlpsLCMS.

See also the tutorial with a real dataset from MetaboLights repository MTBLS665, from beginning to end, including all the steps of the untargeted metabolomics analysis.

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.