UMass Chan Medical School Faculty Publications

UMMS Affiliation

Program in Bioinformatics and Integrative Biology

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Article Preprint


Bioinformatics | Programming Languages and Compilers


Visualizing two-dimensional (2D) embeddings (e.g. UMAP or tSNE) is a key step in interrogating single-cell RNA sequencing (scRNA-Seq) data. Subsequently, users typically iterate between programmatic analyses (e.g. clustering and differential expression) and visual exploration (e.g. coloring cells by interesting features) to uncover biological signals in the data. Interactive tools exist to facilitate visual exploration of embeddings such as performing differential expression on user-selected cells. However, the practical utility of these tools is limited because they don’t support rapid movement of data and results to and from the programming environments where the bulk of data analysis takes place, interrupting the iterative process. Here, we present the Single-cell Interactive Viewer (Sciviewer), a tool that overcomes this limitation by allowing interactive visual interrogation of embeddings from within Python. Beyond differential expression analysis of user-selected cells, Sciviewer implements a novel method to identify genes varying locally along any user-specified direction on the embedding. Sciviewer enables rapid and flexible iteration between interactive and programmatic modes of scRNA-Seq exploration, illustrating a useful approach for analyzing high-dimensional data.


Bioinformatics, Single-cell Interactive Viewer (Sciviewer), Python, single-cell RNA sequencing (scRNA-Seq) data

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

DOI of Published Version



bioRxiv 2021.08.12.455997; doi: Link to preprint on bioRxiv.


This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.

Related Resources

Now published in Bioinformatics, doi: 10.1093/bioinformatics/btab689

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Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.