Protocol for obtaining cancer type and subtype predictions using subSCOPE.

ABSTRACT: We present a protocol for obtaining cancer type and subtype predictions using a machine learning method (subSCOPE). We describe steps for data preparation, subSCOPE setup, and running subSCOPE inference on prepared data. The protocol supports five -omics data types as input (DNA methylation, gene expression, microRNA [miRNA] expression, point mutations, and copy-number variants) and allows individual cancer type and data type selection. For non-The Cancer Genome Atlas (TCGA) cancer samples, it provides subtype-level classification across 26 different TCGA cancer cohorts and 106 subtypes. For complete details on the use and execution of this protocol, please refer to Ellrott et al.¹.

SUBMITTER: Grewal JK 

PROVIDER: S-EPMC12013717 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature