specmine

Version: 1

Website

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

Description

This CRAN package provides tools for metabolomics preprocessing, identification and statistical analysis. Functions for preprocessing include: background correction, baseline correction, offset correction, feature selection, filtering, peak grouping, missing value imputation (K-NN, linear approximation, mean, median or value replacement), mean centering, multiplicative scatter correction, normalisation (sum, median, reference sample or reference feature), scaling (auto, range, pareto or interval) and shift correction (constant, interpolation) . Statistics provided include: ANOVA, clustering, correlation, FC analysis, heatmaps, HCA, k-means clustering, Kruskal-Wallis Test, Kolmogorov-Smirnov Test, linear regression, AUC, multifactor ANOVA, PCA and t-tests. There are also functions for the visualisation of data including box plots, volcano plots and spectra. It can take data in the ChemoSpec and hyperspec formats and convert it for further analysis. xcmsSets can be imported for metabolite identification, using the MAIT package.

Functionality

• Workflow

Instrument Data Type

• NMR
• IR
• UV/VIS
• Raman
• MS/LC-MS
• MS/GC-MS

Approaches

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R (≥ 3.1.0)

Input Formats - Open

Matrix, .csv, .jdx, .dx, .spc

Input Formats - Proprietary

N/A

Published

2015

Last Updated

2015

License

GPL-2 | GPL-3

Paper

http://www.ncbi.nlm.nih.gov/pubmed/26853041

PMID

26853041