Galaxy tools for use within the Deep Metabolome Annotation (DMA) project. Currently only for mass spectrometry data, the tools are primarily for additional data processing (including directed fragmentation tools)
Proceed with caution these tools are were made for use specifically with the Daphnia magna Deep Metabolome Annotation (DMA) project and in some case just for exploratory purposes.
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
Dependencies for these Galaxy tools should be handled by CONDA. The packages used currently for dmatools-galaxy are
- deconrank: A python tool for deconvoluting and ranking precursors to use for fragmentation experiments
- cameraDIMS: A 'hack' of the R package CAMERA so that it can be run on direct infusion datasets (DIMS)
- xcmsWrapper: An R package for various LC-MS processing (e.g blank subtraction, directed fragmentation 'nearline' methods)
The dependencies are currently found on channel tomnl on anaconda
- Thomas N. Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)
- Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)
- Ralf J. M. Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)
- https://github.com/computational-metabolomics/dimspy-galaxy
- https://github.com/computational-metabolomics/mspurity-galaxy
Workflow4metabolomics tools have also been used for DMA. W4M