DIMet 0.1.4

A tool for Differential analysis of Isotope-labeled targeted Metabolomics data

DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data

Introduction

DIMet is a bioinformatics pipeline for differential and time-course analysis of targeted isotope-labeled metabolomics data.

DIMet supports the analysis of full metabolite abundances and isotopologue contributions, and allows to perform it either in the differential comparison mode or as a time-series analysis. As input, DIMet accepts three types of measures: a) isotopologues’ contributions, b) fractional contributions (also known as mean enrichment), c) full metabolites’ abundances. DIMet also offers a pathway-based omics integration through Metabolograms.

Note: DIMet is intended for downstream analysis of tracer metabolomics data that has been corrected for the presence of natural isotopologues.

Formatting and normalisation helper: scripts for formatting and normalization are provided in Tracegroomer.

Installing DIMet

System Requirements

DIMet installation requires an Unix environment with python 3.9. It was tested under Linux and MacOS environments.

Installation

The full installation process should take less than 15 minutes on a standard computer.

Via pip command: pip install dimet

Or if you are a developer working in a local cloned version, you can install: pip install -e .

Code organization

• src/dimet/processing directory contains the implemented high-level analysis scripts that produced the tables for the DIMet paper
• src/dimet/visualization : directory contains the implemented high-level scripts that produced the figures in the DIMet paper
• src/dimet/data directory contains the python classes for data initialization
• src/dimet/method directory contains the python classes for configuration handling
• tests directory contains unit tests
• tools directory contains venv setup scripts.

Running unit tests

• With pytest, by running pytest from DIMet
• Alternatively, place yourself in DIMet/tests and execute python -m unittest

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Documentation

All the details about how to run DIMet can be found on the dedicated Wiki page. Importantly, this is where you will find the information about how to organise the data (folder structure) and how to populate the configuration files to successfully run DIMet.

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Getting help

For any information or help running DIMet, you can get in touch with:

• Johanna Galvis
• Macha Nikolski
• Benjamin Dartigues

LICENSE MIT

Copyright (c) 2023 

Johanna Galvis (1,2)    [e-mail]
Benjamin Dartigues (2)	[e-mail]
Florian Specque (1,2)   [e-mail]
Slim Karkar (1,2)       [e-mail]
Helge Hecht (3,5)       [e-mail]
Bjorn Gruening (4,5)    [e-mail]
Hayssam Soueidan (2)    [e-mail]
Macha Nikolski (1,2)    [e-mail]

(1) CNRS, IBGC - University of Bordeaux,
1, rue Camille Saint-Saens, Bordeaux, France

(2) CBiB - University of Bordeaux,
146, rue Leo Saignat, Bordeaux, France

(3) Spectrometric Data Processing and Analysis,
Masaryk University, Brno, Czech Republic

(4) University of Freiburg, 
Freiburg, Germany

(5) Galaxy Europe

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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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