SciViewer- An interactive browser for visualizing single cell datasets

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Single-cell sequencing improves our ability to understand biological systems at single-cell resolution and can be used to identify novel drug targets and optimal cell-types for target validation. However, tools that can interactively visualize and provide target-centric views of these large datasets are limited. We present SciViewer ( S ingle- c ell I nteractive View er), a novel tool to interactively visualize, annotate and share single-cell datasets. SciViewer allows visualization of cluster, gene and pathway level information such as clustering annotation, differential expression, pathway enrichment, cell-type specificity, cellular composition, normalized gene expression and comparison across datasets. Further, we provide APIs for SciViewer to interact with publicly available pharmacogenomics databases for systematic evaluation of potential novel drug targets. We provide a module for non-programmatic upload of single-cell datasets. SciViewer will be a useful tool for data exploration and target discovery from single-cell datasets. It is available on GitHub ( https://github.com/Dhawal-Jain/SciViewer ).

Authors 8

1. Dhawal S. Jain corresponding
   Affiliation as printed

   Pulmonary Drug Discovery Laboratory, Bayer US LLC. Pharmaceuticals, Research & Development, Boston, MA

2. Sikander Hayat corresponding Aachen Institute of Experimental Medicine and Systems Biology

   RWTH Aachen University

   Affiliation as printed

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen, Germany

   Precision Cardiology Laboratory, Bayer US LLC. Pharmaceuticals, Research & Development, Boston, MA

3. Joydeep Charkaborty

   Bayer (United States)

   Affiliation as printed

   Product Platform Research, Enterprise Platforms and Infrastructure, Bayer US LLC., Morristown, NJ

4. Pooja Srinivasa

   Brigham and Women's Hospital · Harvard University

   Affiliation as printed

   Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

5. Michael H. Cho

   Brigham and Women's Hospital · Harvard University

   Affiliation as printed

   Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

6. Edwin K. Silverman

   Brigham and Women's Hospital · Harvard University

   Affiliation as printed

   Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

7. Rafael Kramann Aachen Institute of Experimental Medicine and Systems Biology

   RWTH Aachen University

   Affiliation as printed

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen, Germany

8. Alexis Laux‐Biehlmann
   Affiliation as printed

   Pulmonary Drug Discovery Laboratory, Bayer US LLC. Pharmaceuticals, Research & Development, Boston, MA