Computational protocol: Multidimensional scaling of diffuse gliomas: application to the 2016 World Health Organization classification system with prognostically relevant molecular subtype discovery

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Protocol publication

[…] Using GISTIC2.0 scores, copy number frequencies of TCGA gliomas were plotted using R software (Version 3.3.2, RProject for Statistical Computing, http://www.r-project.org/) applying the ‘copynumber’ package (http://bioconductor.org/packages/copynumber) using 0.5 and −0.5 as thresholds. […]

Pipeline specifications

Software tools GISTIC, Copynumber
Databases TCGA Data Portal
Application aCGH data analysis
Organisms Homo sapiens
Diseases Brain Neoplasms, Glioblastoma, Glioma, Neoplasms, Central Nervous System Neoplasms