ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR

Sharma, Ankush; Akshay, Akshay; Rogne, Marie; Eskeland, Ragnhild

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 visualisation 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: https://Github.com/EskelandLab/ShinyArchRUiO and a demo server with a haematopoietic tutorial dataset https://cancell.medisin.uio.no/ShinyArchR.UiO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.