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Updated: Jun 16, 2026
Preparation of a Single-Cell Suspension from Mouse Carotid Arteries for Single-Cell Sequencing
Published on: January 19, 2024
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.
Motivation:
Mapping of chromatin accessibility landscapes in single-cells and the integration with gene expression enables a better understanding of gene regulatory mechanisms defining cell identities and cell-fate determination in development and disease. Generally, raw data generated from single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) are deposited in repositories that are generally inaccessible due to lack of in-depth knowledge of computational programming.
Results:
We have developed ShinyArchR.UiO, an R-based shiny app, that facilitates scATAC-seq data accessibility and visualization in a user-friendly, interactive and open-source web interface. ShinyArchR.UiO is an application that can streamline collaborative efforts for interpretation of massive chromatin accessibility datasets and allow for open access data sharing for wider audiences.
Availability And Implementation:
https://Github.com/EskelandLab/ShinyArchRUiO and a demo server with a hematopoietic tutorial dataset https://cancell.medisin.uio.no/ShinyArchR.UiO.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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