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    A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.

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    Author
    Tekman, M; Batut, B; Ostrovsky, A; Antoniewski, C; Clements, D; Ramirez, F; Etherington, GJ; Hotz, H-R; Scholtalbers, J; Manning, JR; ...
    Date
    2020-10-20
    Source Title
    GigaScience
    Publisher
    Oxford University Press (OUP)
    University of Melbourne Author/s
    Doyle, Maria
    Affiliation
    Sir Peter MacCallum Department of Oncology
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Tekman, M., Batut, B., Ostrovsky, A., Antoniewski, C., Clements, D., Ramirez, F., Etherington, G. J., Hotz, H. -R., Scholtalbers, J., Manning, J. R., Bellenger, L., Doyle, M. A., Heydarian, M., Huang, N., Soranzo, N., Moreno, P., Mautner, S., Papatheodorou, I., Nekrutenko, A. ,... Grüning, B. (2020). A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.. Gigascience, 9 (10), https://doi.org/10.1093/gigascience/giaa102.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/251731
    DOI
    10.1093/gigascience/giaa102
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7574357
    Abstract
    BACKGROUND: The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets. RESULTS: Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal. CONCLUSIONS: The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.

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