ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR
ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR
Abstract MotivationMapping 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 inaccessible due to lack of in-depth knowledge of computational programming. ResultsWe 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 a tool that can streamline collaborative efforts for interpretation of massive chromatin accessible data and promotes open access data sharing for wider audiences. Availability and implementationShinyArchR.UiO is available at https://Github.com/EskelandLab/ShinyArchRUiO and a demo server set up with a haematopoietic tutorial dataset: https://cancell.medisin.uio.no/ShinyArchR.UiO ContactAnkush.Sharma@medisin.uio.no & Ragnhild.Eskeland@medisin.uio.no
Eskeland Ragnhild、Akshay Akshay、Rogne Marie、Sharma Ankush
Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo||PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo||Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of OsloUrology Research Laboratory, Department for BioMedical Research DBMR, University of BernInstitute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo||Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of OsloDepartment of Biosciences, University of Oslo||Department of Informatics, University of Oslo||Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo||PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo||Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo
生物科学研究方法、生物科学研究技术基础医学
Chromatin accessibilityscATAC-seqscRNA-seqShiny R packagesingle-cell biologyhigh-throughput sequencing
Eskeland Ragnhild,Akshay Akshay,Rogne Marie,Sharma Ankush.ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2021.06.21.449316.点此复制
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