metabolomics

Version: 0.1.4

Website

https://cran.r-project.org/web/packages/metabolomics/index.html

Description

This CRAN package provides statistical analysis tools for metabolomics data. Functions provided include: HCA, Fold change analysis, heat maps, linear models (either ordinary statistics or empirical Bayes statistics), PCA and volcano plots. It also includes log transformation, missing value replacement and normalisation (median, mean, sum, ref, IS, normalization using optimal selection of multiple internal standards (normis), cross-contribution compensating multiple internal standard normalisation (ccmn) and remove unwanted variation (ruv2)). The ruv2 method of normalisation attempts to capture biological variation: both observed and unobserved. It generates a matrix of unwanted variation using non-changing metabolites, including internal and external standards.

Functionality

• Post-Processing
• Statistical Analysis

Instrument Data Type

• MS
• NMR

Approaches

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

limma, crmn, gplots, R (≥ 3.1.0)

Input Formats - Open

Data frame

Input Formats - Proprietary

N/A

Published

2014

Last Updated

2015

License

GPL-2 | GPL-3

Paper

http://www.ncbi.nlm.nih.gov/pubmed/23150939

PMID

23150939