inst/markdown/methods/TCGASubtype.markdown
In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)
Title: TCGA Molecular Subtypes
Description: Previously published TCGA molecular subtypes from multiple tumor types were collected and compiled into a single matrix. A total of 7,734 TCGA samples were annotated with with molecular subtypes based on TCGA Research Network tumor-specific publications for the following tumor types: ACC, AML, BLCA, BRCA, LGG/GBM , Pan-GI (ESCA/STAD/COAD/READ), HNSC, KICH, KIRC, KIRP, LIHC, LUAD, LUSC, OVCA, PCPG, PRAD, SKCM, THCA, UCEC, and UCS, with publication sources detailed on http://bioinformaticsfmrp.github.io/TCGAbiolinks/subtypes.html. The unified patient-centric matrix contains a comprehensive collection of the subtypes by molecular platform. Each column contains subtype assignments of a particular molecular platform (e.g., mRNA, DNA methylation, protein). We selected the most prominent subtype classification of a particular tumor type based on the corresponding paper recommendation and stored this information in column named Subtype_Selected.The subtype collection matrix and the bibliography associated with them are available within TCGAbiolinks on R/Bioconductor (http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html) (Colaprico et al., 2016) and using the TCGAbiolinksGUI (Silva et al., 2016). The function PanCancerAtlas_subtypes() provides full access to the curated matrix used for this study. The Subtype_Selected column was used for molecular subtypes in this study.
Contributors: Tathiane Malta, Houtan Noushmehr, Antonio Colaprico.
CRI-iAtlas/iatlas-app documentation built on Feb. 7, 2025, 9:02 p.m.
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Title: TCGA Molecular Subtypes
Description: Previously published TCGA molecular subtypes from multiple tumor types were collected and compiled into a single matrix. A total of 7,734 TCGA samples were annotated with with molecular subtypes based on TCGA Research Network tumor-specific publications for the following tumor types: ACC, AML, BLCA, BRCA, LGG/GBM , Pan-GI (ESCA/STAD/COAD/READ), HNSC, KICH, KIRC, KIRP, LIHC, LUAD, LUSC, OVCA, PCPG, PRAD, SKCM, THCA, UCEC, and UCS, with publication sources detailed on http://bioinformaticsfmrp.github.io/TCGAbiolinks/subtypes.html. The unified patient-centric matrix contains a comprehensive collection of the subtypes by molecular platform. Each column contains subtype assignments of a particular molecular platform (e.g., mRNA, DNA methylation, protein). We selected the most prominent subtype classification of a particular tumor type based on the corresponding paper recommendation and stored this information in column named Subtype_Selected.The subtype collection matrix and the bibliography associated with them are available within TCGAbiolinks on R/Bioconductor (http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html) (Colaprico et al., 2016) and using the TCGAbiolinksGUI (Silva et al., 2016). The function PanCancerAtlas_subtypes() provides full access to the curated matrix used for this study. The Subtype_Selected column was used for molecular subtypes in this study.
Contributors: Tathiane Malta, Houtan Noushmehr, Antonio Colaprico.
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