Community forum:
For any questions or support: community.france-bioinformatique.fr/c/workflow4metabolomics/
Galaxy training network: https://training.galaxyproject.org/training-material/topics/metabolomics/
"How to" short notes:
W4E 2021/22 - Toulouse (INRAE -Toxalim)
- Program and trainers
- Resources and supports are available on this repository.
W4E 2020 - Bruxelles (Université Libre de Bruxelles - BOZAR):
- Program and trainers
- Resources and supports are available on this repository.
W4E 2018 - Paris (Pasteur Institute):
| Session | Presentation | Author(s) | |
|---|---|---|---|
| Day 1: Welcome and Introduction | Introduction | Yann Guitton | N/A |
| Galaxy initiation and data management | Gildas Le Corguillé | Download | |
| MS Data conversion | Yann Guitton | Download | |
| Day 2: Metabolomics data Preprocessing | LC-MS data preprocessing | Jean-Francois Martin | Download |
| LC-MS annotation with CAMERA | Yann Guitton | Download | |
| GC-MS data preprocessing | Yann Guitton | Download | |
| NMR data preprocessing | Marie Tremblay-Franco, Cécile Canlet | Download | |
| Signal drift and batch effect correction | Mélanie Pétéra | Download | |
| Day 3: Statistics | Univariate modeling | Marie Tremblay-Franco | Download |
| Multivariate modeling | Etienne Thévenot | Download | |
| Multi Level Analysis | Yann Guitton | Download | |
| Day 4: Annotation | LC/GC-MS Annotation | Yann Guitton | Download |
| Databases in Annotation | Franck Giacomoni | Download | |
| NMR Annotation | Marie Tremblay-Franco, Cécile Canlet | Download | |
| Day 5: "Go Further session" | W4M and perspectives | Etienne Thévenot Yann Guitton Marie Tremblay-Franco Cécile Canlet Franck Giacomoni Julien Saint-Vanne |
Download |
W4E 2017 - Paris :
| session | presentations | Author(s) | |
|---|---|---|---|
| Day 1: Introduction | Introduction to the course | Christophe Caron, W4M Core Team | |
| Galaxy initiation | Gildas Le Corguillé | Download | |
| Day 2: Preprocessing | LC-MS data preprocessing | Jean-Francois Martin | Download |
| LC-MS annotation with CAMERA | Yann Guitton | Download | |
| GC-MS data preprocessing | Yann Guitton | Download | |
| NMR data preprocessing | Marie Tremblay-Franco, Cécile Canlet, Manon Martin | Download | |
| Day 3: Statistics | Filtering and correcting data | Mélanie Petera | Download |
| Univariate satistics | Marie Tremblay-Franco | Download | |
| Multivariate modeling | Etienne Thévenot | Download | |
| Multi Level Analysis | Yann Guitton | Download | |
| Day 4: Annotation |
Databases |
Franck Giacomoni | Download |
| NMR Annotation | Marie Tremblay-Franco, Cécile Canlet | Download | |
| Referencing Histories | Etienne Thévenot | Download |
W4E 2016 :
| W4E courses 2016 | Author(s) | |
|---|---|---|
| Course presentation | Christophe Caron, W4M Core Team | |
| Initiation Galaxy | Gildas Le Corguillé | Download |
| LC-MS - Pre-processing (xcms) | JF Martin | Download |
| GC-MS - Processing | Y. Guitton | Download |
| MS data processing - Filtering and correcting data | Mélanie Petera | Download |
| Statiscal Workflows | Etienne Thévennot, Marie Tremblay-Franco | Download |
|
NMR Annotation |
M. Tremblay-Franco, C. Canlet | Download |
| NMR - Pre-processing | M. Tremblay-Franco, C. Canlet | Download |
W4E 2015
| W4M courses 2015 | Author(s) | |
|---|---|---|
| Course presentation | Christophe Caron, Franck Giacomoni | Download |
| Initiation | Gildas Le Corguillé, Misharl Monsoor, Marion Landi | Download |
| LC-MS - Pre-processing (xcms) | W4M Core Team | Download |
| MS data processing - Filtering and correcting data | W4M Core Team | Download |
| Using Galaxy4Metabolomics - W4M table format for Galaxy | W4M Core Team | Download |
| How to check the format of the 3 .tsv tables | Etienne Thévenot | Download |
| How to perform statistical analysis ? - Introduction | Etienne Thévenot, Marie Tremblay-Franco, Mélanie Pétéra, Gildas Le Corguillé | Download |
| How to perform statistical analysis ? - Exploratory data analysis | Etienne Thévenot, Mélanie Pétéra, Jean-François Martin, Gildas Le Corguillé | Download |
| How to perform statistical analysis ? - PCA analysis and (O)PLS(-DA) modelling | Etienne Thévenot | Download |
| Les banques d'annotation - Annotation | Yann Guitton, Franck Giacomoni | Download |
HOWTO
| CATEGORY | FIELD | Description | |
|---|---|---|---|
|
Galaxy |
Prepare input datasets |
||
|
Galaxy |
Use single files as input and run xcmsSet in parallel |
||
| Galaxy | Import datasets | Download | |
| Galaxy | Cleanup datasets | Download | |
| Galaxy | Build And Configure A Workflow | Download | |
| Galaxy | Share Histories And Workflows | Download | |
| Galaxy | Export/Import Workflows&Histories | Download | |
| Preprocessing | LC-MS | Perform Preprocessing using XCMS | Download |
| Quality Control | Common | Format Data For Postprocessing | Download |
| Batch correction | LC-MS and GC-MS | Perform Drift And Batch Correction | Download |
| Statistics | Common | Perform Univariate Analyzes | Download |
| Statistics | Common | Perform Multivariate Analyzes | Download |
| Annotation | LC-MS | Perform LCMS Annotations | Download |
| Annotation | GC-MS | Use NIST | Download |