Academic Journal
Plotgardener App: a graphical interface for publication-ready genomic visualization.
| Τίτλος: | Plotgardener App: a graphical interface for publication-ready genomic visualization. |
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| Συγγραφείς: | Vemuri RS; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Berhanu A; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Kenney GE; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Parker SM; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Phillips JT; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Flores JP; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Rashid T; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States., Phanstiel DH; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.; Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States. |
| Πηγή: | Bioinformatics (Oxford, England) [Bioinformatics] 2026 Aug 31; Vol. 42 (9). |
| Τύπος έκδοσης: | Journal Article; Research Support, N.I.H., Extramural |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford : Oxford University Press, c1998- |
| Ιατρικοί όροι (MeSH): | Genomics*/methods , Software* , User-Computer Interface* , Computer Graphics* |
| Περίληψη: | Summary: Plotgardener is an R package used for generating high-quality genomic visualizations. Despite its broad range of functions and versatility, its reliance on code presents a barrier for many potential users. To address this, we developed a macOS desktop application version of Plotgardener that enables users to create publication-ready genomic plots with no programming experience. The application employs a modular architecture comprising an Electron.js backend, a React frontend, and a Python parser that dynamically analyzes the Plotgardener package to ensure interface fields remain synchronized with package updates. By lowering the technical barrier to advanced genomic visualization, the Plotgardener desktop application broadens access to powerful visualization workflows for researchers and clinicians. Availability: The current release of the Plotgardener App is an open source macOS desktop application built with Electron (Node.js), featuring a React frontend and a Python-based parser. The download link is available at https://phanstiellab.github.io/plotgardener/articles/guides/plotgardenerApp.html and on Zenodo (doi: https://doi.org/10.5281/zenodo.21684228). The source code is hosted on GitHub at https://github.com/rishabhsvemuri/ThePlotgardenerApp. (© The Author(s) 2026. Published by Oxford University Press.) |
| References: | Bioinformatics. 2022 Mar 28;38(7):2042-2045. (PMID: 35134826) Bioinformatics. 2009 Jan 1;25(1):119-20. (PMID: 18990721) Cell Syst. 2016 Jul;3(1):99-101. (PMID: 27467250) Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6. (PMID: 21045057) Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153) Nucleic Acids Res. 2025 Jul 7;53(W1):W554-W561. (PMID: 40322916) Nat Biotechnol. 2011 Jan;29(1):24-6. (PMID: 21221095) Genome Biol. 2018 Aug 24;19(1):125. (PMID: 30143029) Nucleic Acids Res. 2012 Jan;40(2):e12. (PMID: 22102585) Nat Methods. 2014 Sep;11(9):938-40. (PMID: 25086505) |
| Grant Information: | R35 GM128645 United States GM NIGMS NIH HHS; R35-GM128645 United States NH NIH HHS |
| Entry Date(s): | Date Created: 20260828 Date Completed: 20260909 Latest Revision: 20260912 |
| Update Code: | 20260912 |
| PubMed Central ID: | PMC13557622 |
| DOI: | 10.1093/bioinformatics/btag649 |
| PMID: | 42664080 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 1367-4811 |
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| DOI: | 10.1093/bioinformatics/btag649 |