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Lookup NU author(s): James HackingORCiD, Dr Dean Thompson, Dr Ed Schwalbe, Professor Steven CliffordORCiD, Dr Daniel Williamson
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2023 The Authors. Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be projected onto new sample data analyzed via RNA-sequencing. We then detail procedures for reverse engineering a continuum score for samples analyzed via DNA methylation microarray using a random forest classifier.
Author(s): Hacking JPR, Thompson D, Schwalbe EC, Clifford SC, Williamson D
Publication type: Article
Publication status: Published
Journal: STAR Protocols
Year: 2023
Volume: 4
Issue: 3
Print publication date: 15/09/2023
Online publication date: 11/08/2023
Acceptance date: 02/04/2018
Date deposited: 15/09/2023
ISSN (electronic): 2666-1667
Publisher: Cell Press
URL: https://doi.org/10.1016/j.xpro.2023.102509
DOI: 10.1016/j.xpro.2023.102509
Data Access Statement: All data and code required to complete this protocol are available at https://github.com/hackingjpr/Group3-4App
PubMed id: 37573504
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