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Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray

Lookup NU author(s): James HackingORCiD, Dr Dean Thompson, Dr Ed Schwalbe, Professor Steven CliffordORCiD, Dr Daniel WilliamsonORCiD

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 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.

Publication metadata

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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