recetox/training-material

A collection of Galaxy-related training material

training-material's Issues

GTN GC-MS with xcms: update

The GC-MS training with xcms should be updated - it should reflect new version of matchms, and possibly also RAMClustR.

GTN rcx-aplcms: create picture illustrating weak signal

We need to include a figure showing recovery of weak signals. What would be nice is to have 3D surface plot (mz, rt, intensity) with a peak with low intensity. This could be then highlighted and compared to a metadata aligned table as the missing feature.

GTN rcx-aplcms: Section on weaker signal recovery

Relevant Papers:

• 10.1038/s41598-017-19120-0
• 10.1007/s11306-011-0366-4
• 10.1093/bioinformatics/btp291
• 10.1021/ac051437y
• 10.1186/1471-2105-9-504

GTN rcx-aplcms: Section on data conversion (ThermoRawFileConverter)

Relevant Papers:

• 10.1016/j.trac.2013.07.010
• 10.1002/rcm.9036
• 10.1038/nbt.2377
• 10.1074/mcp.R110.000133

GTN: Molecular networking with matchms & cytoscape

This galaxy training should describe how - after obtaining (annotated) spectra in msp format - we can use matchms for molecular networking and similarity computation as well as filtering of our msp libraries.

• Get started with GitPod and GTN training
• Assemble preliminary workflow
• Section on molecular networking
• Section on spectral matching & MSP data
• Section on networking tool -> future
• Section on cytoscape in Galaxy

Peak detection with recetox-aplcms Galaxy Training

This should be a small Galaxy training giving a more in-depth description on how to use the recetox-aplcms tool for peak detection for GC & LC-MS data, similar to the original tutorial here.

• GTN rcx-apclms: write introduction about package
• #7
• #6
• GTN rcx-aplcms: Section on peak detection step
• #4
• GTN rcx-aplcms: Section on peak alignment
• #5
• GTN rcx-aplcms: Section on outputs

GC-HRMS data processing Galaxy Training

• #1
• Section on deconvolution with RAMClustR
• Section on batch correction with WaveICA
• Section on RI addition with RIAssigner
• Section on matching with matchms
• Section on output filtering and representation

GTN rcx-aplcms: Write section on the data (GC + LC)

GTN rcx-aplcms: Section on retention time correction

Relevant papers:

• 10.1186/1471-2105-13-214
• 10.1186/1471-2105-9-375
• 10.7551/mitpress/7503.003.0118
• 10.1093/bioinformatics/btp291