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ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using
Ankush Sharma1,2,3,4,5, Akshay Akshay6, Marie Rogne3,5
1Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
Bioinformatics (Oxford, England)
|September 29, 2021
Summary
ShinyArchR.UiO is a user-friendly R-based app making single-cell ATAC sequencing (scATAC-seq) data accessible and visual. This tool enhances collaboration and data sharing for interpreting complex chromatin accessibility datasets.
Area of Science:
- Genomics
- Computational Biology
- Epigenetics
Background:
- Single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) generates crucial data for understanding gene regulation.
- Interpreting scATAC-seq data is challenging due to computational complexity and data inaccessibility.
- Lack of user-friendly tools hinders broader analysis and collaboration in single-cell epigenomics.
Purpose of the Study:
- To develop an accessible and interactive platform for scATAC-seq data analysis.
- To facilitate visualization and interpretation of chromatin accessibility landscapes.
- To promote open-access data sharing and collaborative research in single-cell epigenomics.
Main Methods:
- Development of ShinyArchR.UiO, an R-based Shiny application.
- Implementation of a user-friendly, interactive, and open-source web interface.
- Integration of visualization tools for scATAC-seq data exploration.
Main Results:
- ShinyArchR.UiO provides a streamlined workflow for scATAC-seq data interpretation.
- The application enhances data accessibility for researchers without extensive programming skills.
- Facilitates collaborative analysis and open sharing of chromatin accessibility datasets.
Conclusions:
- ShinyArchR.UiO democratizes scATAC-seq data analysis, enabling wider scientific community engagement.
- The tool supports robust interpretation of single-cell chromatin accessibility data.
- Promotes collaborative research and accelerates discoveries in developmental and disease contexts.
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