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MiSDEED: a synthetic multi-omics engine for microbiome power analysis and study design

View ORCID ProfilePhilippe Chlenski, Melody Hsu, Itsik Pe’er
doi: https://doi.org/10.1101/2021.08.09.455682
Philippe Chlenski
1Department of Computer Science, Columbia University, New York, NY 10027, USA
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  • For correspondence: pchlenski@gmail.com
Melody Hsu
1Department of Computer Science, Columbia University, New York, NY 10027, USA
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Itsik Pe’er
1Department of Computer Science, Columbia University, New York, NY 10027, USA
2Department of Systems Biology, Columbia University, New York, NY 10027, USA
3Data Science Institute, Columbia University, New York, NY 10027, USA
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Abstract

Summary MiSDEED is a command-line tool for generating synthetic longitudinal multi-omics data from simulated microbial environments. It generates relative-abundance timecourses under perturbations for an arbitrary number of samples and patients. All simulation parameters are exposed to the user to facilitate rapid power analysis and aid in study design. Users who want additional flexibility may also use MiSDEED as a Python package.

Availability and implementation MiSDEED is written in Python and is freely available at https://github.com/pchlenski/misdeed.

Contact pac{at}cs.columbia.edu

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.github.com/pchlenski/misdeed

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 10, 2021.
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MiSDEED: a synthetic multi-omics engine for microbiome power analysis and study design
Philippe Chlenski, Melody Hsu, Itsik Pe’er
bioRxiv 2021.08.09.455682; doi: https://doi.org/10.1101/2021.08.09.455682
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MiSDEED: a synthetic multi-omics engine for microbiome power analysis and study design
Philippe Chlenski, Melody Hsu, Itsik Pe’er
bioRxiv 2021.08.09.455682; doi: https://doi.org/10.1101/2021.08.09.455682

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