Scope
ShinyArchR.UiO is a user-friendly, integrative open-source Shiny-based web app using R programming for visualization of massive single-cell chromatin accessibility data (scATAC-seq) based on ArchR (Corces et al., 2021).
Approach
The ArchR objects saved in folders along with HDF5 formatted Arrow files are used for input in ShinyArchR.UiO.
Data Visualization of ShinyArchR.UiO:
- scATAC-seq clusters, unconstrained and constrained clusters on integrated reduced dimensions UMAP from ArchR objects
- Peaks using plot browser tracks on clusters on scATAC-seq modality
- Peaks2Genelinks tracks on single-cell RNA sequencing (scRNA-seq) integrated data with scATAC-seq using plot browser tracks. The co-accessibility among the genes can be visualized in the bottom panel
- Heatmaps of pseudo time trajectory
- Heatmaps of top 50 markers Peak2Genelinks in scATAC-seq and scRNA-seq
Contributions and Citation info
ShinyArchR.UiO software is developed at Chromatin Biology Lab at University of Oslo, as an open-source project mainly under the GPL license version 3 (see source code for details).
If ShinyArchR.UiO in any way help you in visualizing and sharing your research work such that it warrants a citation, please cite the ShinyArchR.UiO preprint in BioRXiv or the final publication.