shinyUMAP: an online tool for promoting understanding of single cell omics data visualization
Overview
Paper Summary
This paper introduces shinyUMAP, an online tool that allows users to interactively explore and adjust parameters for UMAP, a common dimensionality reduction technique used for visualizing single-cell omics data. By manipulating parameters and observing their impact on data visualization, users can gain a deeper understanding of UMAP's limitations and avoid misinterpretations.
Explain Like I'm Five
Imagine trying to flatten a crumpled piece of paper. ShinyUMAP lets you see how different flattening methods change how the drawing on the paper looks.
Possible Conflicts of Interest
None identified. The authors declare no conflicts of interest and the research was partially funded by NIH grants, which are generally considered transparent funding sources.
Identified Limitations
Rating Explanation
This paper presents a useful tool that addresses a practical challenge in single-cell data analysis: understanding and properly using UMAP. The interactive nature of shinyUMAP and its potential for educational purposes are significant strengths. However, the limitations related to data size and Python-based implementation slightly lower the rating. Overall, the tool fills a need in the community and contributes to more informed interpretations of UMAP visualizations.
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