Dimension Reduction scClusters UMAPs
Users can view and compare side-by-side UMAPs' representing identified scATAC-seq clusters, origin of sample, unconstrained and constrained integration with scRNA-seq datasets, and integrated remapped clusters.
Peak browser of scATAC-seq clusters
Users can view and compare the single-cell chromatin accessibility data in scalable peak browser view along with co-accessibility of peaks on scATAC-seq modality.
Browser view of Peak2GeneLinks
User can visualize genome accessibility tracks of marker genes with peak co-accessibility
Feature of interest : Dimensionality Reduction UMAPs
Users can view and compare side-by-side UMAPs representing features of interest in GeneScoreMatrix, GeneIntegrationMatrix or MotifMatrix with a representative sequence logo. Download list of Motif positions.
ArchR defined trajectory heatmaps
Users can visualize heatmaps from ArchR defined trajectory analysis on four different computed matrices.
Peak2GeneLinks heatmaps
Users can view Peak2GeneLinks identified across the dataset with ArchR.

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.