Galaxy-M

Version: 1

Website

https://GitHub.com/Viant-Metabolomics/Galaxy-M

Description

These are metabolomics tools for Galaxy. It includes Galaxy installations of MI-PACK, XCMS and CAMERA. PLS-Toolbox is a commercial MATLAB toolbox for chemometric multivariate analysis that can also be optionally installed. Galaxy-M is designed for use in the analysis of LC-MS and DI-MS metabolomics data. Functions from XCMS can be used for peak picking and retention time alignment. CAMERA is used for adduct annotation. A number imputation techniques are included: small value replacement, mean replacement, median replacement, KNN imputation (SimStitch) and BPCA imputation. Either TIC or PQN normalisation can be applied. Features and samples can be filtered by the number of missing values they contain. Noise filling can be applied. General logarithm transformation is also available. Features below a user-specified RSD threshold across QC samples can be removed for quality assurance. Batch correction and peak outlier detection can also be applied. PCA and univariate (2-tailed t-test/1-way ANOVA) statistical analysis is provided. MI-PACK provides empirical formula identification.

Functionality

• Workflow

Instrument Data Type

• MS/LC-MS
• MS/DI-MS

Approaches

Computer Skills

Medium

Software Type

Packages

Interface

Galaxy-based

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R, Python, MATLAB

Dependencies

Python 2.7, numpy 1.8.1, scipy 0.14.0, comptypes 0.6.1, MSFileReader 3.0, MI-PACK, Galaxy, MATLAB Complier Runtime, R (≥ 3.1), Hmisc, XCMS, CAMERA

Input Formats - Open

mzData, mzML, mzXML, netCDF

Input Formats - Proprietary

N/A

Published

2015

Last Updated

2016

License

GPL-3

Paper

https://www.ncbi.nlm.nih.gov/pubmed/26913198

PMID

26913198