tracegroomer 0.1.4

Convert and normalise metabolomics data formats (preprocessing for DIMet)

TraceGroomer

TraceGroomer is a solution for formatting and normalising isotope-labeled (a.k.a Tracer) Metabolomics given file(s), to produce the tabular files which are ready for DIMet tool.

Not only one, but several input formats are accepted by TraceGroomer!: these input formats are described in detail (visit the Wiki link provided in our documentation section), e.g. IsoCor output files are currently supported.

TraceGroomer processes your data in seconds!

For any type of the supported inputs, TraceGroomer generates an independent file for each type of quantification: i) total metabolite abundances ii) Isotopologues iii) Isotopologues' proportions and iv) mean enrichment (a.k.a fractional contributions).

Advantages of using TraceGroomer for preparing your data for DIMet:

• if only Isotopologues' absolute values are provided, TraceGroomer generates all the other quantifications automatically.
• fast, automatic formatting is performed, as well as the normalization chosen by the user: whether by the amount of material and/or by an internal standard.
• useful advanced options are offered (e.g. different modalities of normalization by the amount of material).

Note : TraceGroomer does not correct for naturally occurring isotopologues. Your data must be already processed by another software that performs such correction (e.g. IsoCor).

[!IMPORTANT] When using TraceGroomer, please cite:

Galvis J, Guyon J, Dartigues B, Hecht H, Grüning B, Specque F, Soueidan H, Karkar S, Daubon T, Nikolski M. DIMet: An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data. Bioinformatics 2024; 40(5) btae282. https://doi.org/10.1093/bioinformatics/btae282

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Requirements

TraceGroomer requires Python 3.10+. Running in a virtual environment is highly recommended.

Install it via pip: pip install tracegroomer

Tracegroomer is also available as a conda package

Alternatively, if you are a developer, you can do a local install:

Local install of TraceGroomer ^{_{(click to show/hide)}}

For a local install, clone this repository, make sure you have activated your virtual environment with Python 3.10+ (source MY_VIRTUAL_ENV/bin/activate), with poetry installed.

Then install dependencies: locate yourself in TraceGroomer and run

poetry install

After this, the tool is ready to use:

python -m tracegroomer --help

Documentation

All the details about how to use TraceGroomer can be found on the dedicated Wiki page. This is where you will find the information of the supported formats, examples, and how to run TraceGroomer.

Getting help

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

• Johanna Galvis
• Macha Nikolski
• Benjamin Dartigues

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LICENSE MIT

Copyright (c) 2024

Johanna Galvis (1,2)    [e-mail]
Benjamin Dartigues (2)	[e-mail]
Slim Karkar (1,2)       [e-mail]
Helge Hecht (3,5)       [e-mail]
Bjorn Gruening (4,5)    [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) RECETOX
Faculty of Science, Masaryk University, Kotlářksá 2, 611 37 Brno, Czech Republic

(4) University of Freiburg,
Freiburg, Germany

(5) Galaxy Europe

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

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

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.