This repository contains material for the metabolomics practical tutorial part of the **Medical Genomics** course to be held at the INSA Lyon engineering school (French National Institute of Applied Sciences of Lyon) in the Biosciences MSc curriculum during the Fall 2020 (https://biosciences.insa-lyon.fr/en/)
Here you will use interactive Jupyter Notebooks run in Binder to test an example of a metabolomics data analysis workflow.
Here we present you two Jupyter Notebook one for a LC-MS data processing and one for a data analysis workflow:
- LC-MS data processing: "tutorial_XCMS.ipynb" This notebook requires that you have Jupyter with R 3.6.3 kernel setup (the R notebook version will also be available) and install Bioconductor by running the script install.R. The files are available in XCMS_processing The data to be used is available to download here: https://transferxl.com/08QhG2QvpLmSz
This notebook has some exercises at the end without solutions in the folder "XCMS_processing" https://github.com/adam-amara/Metabolomics-tutorial/tree/main/XCMS_processing and with solutions in the subfolder "solution" https://github.com/adam-amara/Metabolomics-tutorial/tree/main/XCMS_processing/solution
- NMR & LC-MS data analysis: "Tutorial_NMR_and_LCMS.ipynb"
Notebook on Metabolomics data analysis workflow
You can access and run this interactive notebook online
- Step 1: click on the Binder linker / wait for Binder to create an environment
- Step 2: Click on the Notebook: "Tutorial_NMR_LC-MS.ipynb"
- Step 3: You can use the notebook and run snippets of codes or the whole notebook at once
If you want to run this notebook on your local machine make sure to install Jupyter, Python, and the dependencies used for this tutorial (see Notebook Part 1 to find the libraries used)
The data analysis tutorial is inspired and derived from the Jupyter Notebooks tutorial based on publication: "Toward Collaborative Open Data Science in Metabolomics using Jupyter Notebooks and Cloud Computing". SI_Mendez_etal_2019
Available in Github: https://github.com/CIMCB/MetabWorkflowTutorial