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.
The package includes the following tools:
- Import - Import of NMR data (from Bruker raw files)
- Bruker to csv
- Bruker to nmrML
- Peak Picking
- Spectra alignment
- Make factor template (for grouping observations)
- Stats - univariate and multivariate statistics
- one-way ANOVA
- Principal component analysis (PCA)
- Partial least squares discriminant analysis (PLS-DA)
- 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)
Most of the tools are implemented in R and Python. Following packages are required in order to run all the tools:
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.