Tools for Analysis of Metabolomic NMR
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README.md

README.md

Tools for Analysis of MEtabolomic NMR (tameNMR)

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. Import - Import of NMR data (from Bruker raw files)
    • Bruker to csv
    • Bruker to nmrML
  2. ProcessSpectra
    • Normalisation
    • Peak Picking
    • Spectra alignment
    • Binning
  3. ProcessData
    • Scaling
    • Make factor template (for grouping observations)
  4. Stats - univariate and multivariate statistics
    • t-tests
    • one-way ANOVA
    • Principal component analysis (PCA)
    • Partial least squares discriminant analysis (PLS-DA)
  5. 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)

Implementation details

Most of the tools are implemented in R and Python. Following packages are required in order to run all the tools:

  1. R
    • ggplot2
    • MassSpecWavelet
    • speaq
  2. Python
    • numpy
    • nmrglue
    • pandas

In the development version the tools use csv files for input and output. However we aim to use [nmrML] (http://nmrml.org) data format for all data processing steps. This is currently being added into the tools.

The nmrML format (http://nmrml.org) has been developed as a uniform NMR data storage and exchange standard and is being rapidly adopted in the field.

This is a development version of tameNMR that changes quite often.

Stable version will be available soon.