OptiLCMS

Introduction

OptiLCMS is an R package providing an optimized LC-MS raw data processing workflow. The source code of the "MS Spectral Processing" Module in MetaboAnalyst is contained here. OptiLCMS can be used to repeat the results generated by MetaboAnalyst at local, and is also optionally dependent by MetaboAnalystR to

Installation

There are 3 typical approaches provided for users to install this package as below.

Install from CRAN

# Install from CRAN repository
install.packages("OptiLCMS")

Install from Bioconductor

# Install from Bioconductor repository, Please make sure 'Bioconductor' has been installed first
BiocManager::install("OptiLCMS")

Install devlopement (beta) version

# Latest features could only be obtained from this approach, make sure 'devtools' installed first
devtools::install_github("xia-lab/OptiLCMS", build = TRUE, build_vignettes = FALSE, build_manual =T)

Tutorial

A step-by-step tutorial will be prepared for users to start their analysis by following them.

Citation

OptiLCMS package has been developed by the XiaLab at McGill University. If you use the R package, please cite us:

• Pang, Z., Chong, J., Li, S. and Xia, J. (2020) MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics. Metabolites 10(5) 186 link

From within R:

citation("OptiLCMS")

New features requests & Bugs reports

To inform us of any bugs or requests, please open a new issue (and @ Zhiqiang-PANG !!) or send an email to [email protected].