trellixvulnteam / tamenmr-phenomenal_brwh

tameNMR version for PhenoMeNal project

Tools for Analysis of MEtabolomic NMR (tameNMR)

This version is meant for the PhenoMenal project (link)

tameNMR is a suite of tools for processing and analysis of NMR data from metabolomics experiments. It is designed as a set of command line programs to be used as standalone tools or for design of automated workflows in Galaxy (galaxyproject.org) framework.

Structure

The package includes the following tools:

1. ProcessSpectra
   • Normalisation
   • Peak Picking
   • Spectra alignment
   • Preparation of pattern files for binning
   • Binning
2. ProcessData
   • Scaling
   • Normalisation of data tables
   • Data transformations
   • Make factor template (for grouping observations)
3. Stats - univariate and multivariate statistics
   • t-tests
   • one-way ANOVA
   • Principal component analysis (PCA)
   • Partial least squares discriminant analysis (PLS-DA)
4. Plots - various plotting tools for:
   • Raw NMR spectra
   • Quantiles of spectra
   • Significant bins (p-values from t-tests of ANOVA)
   • Significant bins (mean value comparison)