Preparing glycomics data for robust statistical analysis with GlyCompareCT
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, name...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S266616672300120X |
| _version_ | 1797870496753123328 |
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| author | Yujie Zhang Sridevi Krishnan Bokan Bao Austin W.T. Chiang James T. Sorrentino Song-Min Schinn Benjamin P. Kellman Nathan E. Lewis |
| author_facet | Yujie Zhang Sridevi Krishnan Bokan Bao Austin W.T. Chiang James T. Sorrentino Song-Min Schinn Benjamin P. Kellman Nathan E. Lewis |
| author_sort | Yujie Zhang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T00:29:26Z |
| format | Article |
| id | doaj.art-0c1ce89d9d2a4bf49a6cf9e4522100a0 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-10T00:29:26Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-0c1ce89d9d2a4bf49a6cf9e4522100a02023-03-15T04:29:03ZengElsevierSTAR Protocols2666-16672023-06-0142102162Preparing glycomics data for robust statistical analysis with GlyCompareCTYujie Zhang0Sridevi Krishnan1Bokan Bao2Austin W.T. Chiang3James T. Sorrentino4Song-Min Schinn5Benjamin P. Kellman6Nathan E. Lewis7Department 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, USADepartment of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USADepartment 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, USADepartment of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USADepartment 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, USADepartment 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, USADepartment 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 authorDepartment 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 authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S266616672300120XBioinformaticsMolecular BiologySystems Biology |
| spellingShingle | Yujie Zhang Sridevi Krishnan Bokan Bao Austin W.T. Chiang James T. Sorrentino Song-Min Schinn Benjamin P. Kellman Nathan E. Lewis Preparing glycomics data for robust statistical analysis with GlyCompareCT STAR Protocols Bioinformatics Molecular Biology Systems Biology |
| title | Preparing glycomics data for robust statistical analysis with GlyCompareCT |
| title_full | Preparing glycomics data for robust statistical analysis with GlyCompareCT |
| title_fullStr | Preparing glycomics data for robust statistical analysis with GlyCompareCT |
| title_full_unstemmed | Preparing glycomics data for robust statistical analysis with GlyCompareCT |
| title_short | Preparing glycomics data for robust statistical analysis with GlyCompareCT |
| title_sort | preparing glycomics data for robust statistical analysis with glycomparect |
| topic | Bioinformatics Molecular Biology Systems Biology |
| url | http://www.sciencedirect.com/science/article/pii/S266616672300120X |
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