ShinyArchR UiO

ShinyArchR UiO provides interactive visualization and analysis of single-cell chromatin accessibility datasets from Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) to support identification of regulatory elements and integration with gene expression profiles.

Key Features:

• scATAC-seq analysis: Processing and visualization capabilities for single-cell chromatin accessibility datasets generated by Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq).
• Gene expression integration: Integration of scATAC-seq data with gene expression profiles to support inference of regulatory relationships between chromatin accessibility and transcription.
• Regulatory element identification: Detection and exploration of regulatory elements and their associations with gene expression at single-cell resolution.
• ArchR integration: Leverages the ArchR framework for single-cell chromatin accessibility analysis to implement core analytical methods.
• Implementation technologies: Implemented in R and built on the Shiny framework for interactive computational analysis.

Scientific Applications:

• Chromatin accessibility mapping: Mapping chromatin accessibility landscapes at single-cell resolution to define cellular identities.
• Regulatory network inference: Elucidating regulatory networks by linking accessibility of regulatory elements to gene expression profiles.
• Development and disease research: Investigating cell fate decisions and mechanisms relevant to developmental biology and disease through combined chromatin accessibility and expression analysis.

Methodology:

Uses the ArchR framework to process and visualize scATAC-seq datasets and is implemented in R using the Shiny framework.