Preparing glycomics data for robust statistical analysis with GlyCompareCT

Yujie Zhang; Sridevi Krishnan; Bokan Bao; Austin W.T. Chiang; James T. Sorrentino; Song-Min Schinn; Benjamin P. Kellman; Nathan E. Lewis

STAR Protocols (Jun 2023)

Preparing glycomics data for robust statistical analysis with GlyCompareCT

Yujie Zhang,
Sridevi Krishnan,
Bokan Bao,
Austin W.T. Chiang,
James T. Sorrentino,
Song-Min Schinn,
Benjamin P. Kellman,
Nathan E. Lewis

Affiliations

Yujie Zhang: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
Sridevi Krishnan: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
Bokan Bao: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
Austin W.T. Chiang: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
James T. Sorrentino: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
Song-Min Schinn: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA
Benjamin P. Kellman: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Augment Biologics, 9450 SW Gemini Dr. #46664, Beaverton, OR 97008, USA; Corresponding author
Nathan E. Lewis: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Corresponding author

Journal volume & issue: Vol. 4, no. 2
p. 102162

Abstract

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Summary: GlyCompareCT is a portable command-line tool to facilitate downstream glycomic data analyses, by addressing data inherent sparsity and non-independence. Inputting glycan abundances, users can run GlyCompareCT with one line of code to obtain the abundances of a minimal substructure set, named glycomotif, thereby quantifying hidden biosynthetic relationships between measured glycans. Optional parameters tuning and annotation are supported for personal preference.For complete details on the use and execution of this protocol, please refer to Bao et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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