Evidence map›Paper›PMID 42664080›Full record

ArticleBioinformatics (Oxford, England)2026

Plotgardener App: a graphical interface for publication-ready genomic visualization.

Rishabh Sharma Vemuri, Abiye Berhanu, Grace E Kenney, Sarah M Parker, Jeffrey T Phillips, J P Flores, Tooba Rashid, Douglas H Phanstiel

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Rishabh Sharma VemuriDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
Abiye BerhanuDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
Grace E KenneyCurriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.ORCID 0009-0009-6308-3150
Sarah M ParkerCurriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.ORCID 0000-0002-2700-3979
Jeffrey T PhillipsDepartment of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
J P FloresCurriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
Tooba RashidCurriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
Douglas H PhanstielCurriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.ORCID 0000-0003-2123-0051

Funding

Mechanisms of Dynamic Chromatin Looping During Differentiation - Common Fund Data SupplementR35GM128645 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Douglas H. Phanstiel · 2018 to 2026
$3.4M
NIGMS NIH HHS R35 GM128645NIH HHS R35-GM128645
6 · The paper itself

Abstract

summaryPlotgardener 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.

Indexed as

Computer GraphicsGenomicsSoftwareUser-Computer Interface

Identifiers

PMID42664080
PMCPMC13557622

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.