HOW TO

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:

  • What is the 3 tables format ? [PDF]
  • How to search in GCMS Data? [PDF]

 

W4E 2021/22 - Toulouse (INRAE -Toxalim)

 

W4E 2020 - Bruxelles (Université Libre de Bruxelles - BOZAR):

 

W4E 2018 - Paris (Pasteur Institute):

Session Presentation Author(s) PDF
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) PDF
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) PDF
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) PDF
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 PDF

Galaxy

 

Prepare input datasets

Download

Galaxy

 

Use single files as input and run xcmsSet in parallel

Download video

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