# OptiLCMS

**Repository Path**: arhelion/OptiLCMS

## Basic Information

- **Project Name**: OptiLCMS
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-10-28
- **Last Updated**: 2024-10-28

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# 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](https://dev.metaboanalyst.ca/MetaboAnalyst/upload/SpectraUpload.xhtml) is contained here. OptiLCMS can be used to repeat the results generated by MetaboAnalyst at local, and is also optionally dependent by MetaboAnalystR to perform raw MS data processing. 


### Installation

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

#### (a.) Install devlopement (beta) version

```R
# 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 =TRUE)

```

#### (b.) Install from the local R tar package

Download the latest version from the following Options:

[v1.1.0](https://drive.google.com/file/d/1jdy3WQvNNr8qapWuJ6ZHwcoyf7fX4ywe/view?usp=share_link);


```R
# Remember to replace the PATH_TO_TAR as the right path of your downloaded package (OptiLCMS_1.1.X.tar.gz).
install.packages(PATH_TO_TAR, repos = NULL, type="source")

```


### Tutorial

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

### Citation

OptiLCMS package has been developed by the [XiaLab](https://www.xialab.ca/) 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](https://doi.org/10.3390/metabo10050186)

*From within R:*

```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 zhiqiang.pang@mail.mcgill.ca.