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

View ORCID ProfileAnkush Sharma, Akshay Akshay, View ORCID ProfileMarie Rogne, View ORCID ProfileRagnhild Eskeland
doi: https://doi.org/10.1101/2021.06.21.449316
Ankush Sharma
1Department of Biosciences, University of Oslo, Norway
2Department of Informatics, University of Oslo, Norway
4Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Norway
5PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway
6Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
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  • ORCID record for Ankush Sharma
  • For correspondence: Ankush.Sharma@medisin.uio.no Ragnhild.Eskeland@medisin.uio.no
Akshay Akshay
3Urology Research Laboratory, Department for BioMedical Research DBMR, University of Bern, Bern, Switzerland
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Marie Rogne
4Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Norway
6Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
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Ragnhild Eskeland
4Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Norway
5PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway
6Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
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  • ORCID record for Ragnhild Eskeland
  • For correspondence: Ankush.Sharma@medisin.uio.no Ragnhild.Eskeland@medisin.uio.no
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Abstract

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 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 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 implementation ShinyArchR.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

Contact Ankush.Sharma{at}medisin.uio.no & Ragnhild.Eskeland{at}medisin.uio.no

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • To update links to Github and server. Updated Supplemental data.

  • https://cancell.medisin.uio.no/ShinyArchR.UiO

  • https://Github.com/EskelandLab/ShinyArchRUiO

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 02, 2021.
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ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR
Ankush Sharma, Akshay Akshay, Marie Rogne, Ragnhild Eskeland
bioRxiv 2021.06.21.449316; doi: https://doi.org/10.1101/2021.06.21.449316
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ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR
Ankush Sharma, Akshay Akshay, Marie Rogne, Ragnhild Eskeland
bioRxiv 2021.06.21.449316; doi: https://doi.org/10.1101/2021.06.21.449316

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