canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
Introduction | Installation | Suplementary librairies (Not R packages) | dependencies from Bioconductor | Starting Window | Setting Workspace | Main Window | Gene List | Clinical Data | Mutation | Methylation | Profiles | PhenoTest | Examples | GSEA-R | Preprocessing of Exprimental Data | Molecular Signatures DataBase | MSigDB Collection | Study: Uterine Corpus Endometrioid Carcinoma (TCGA, Nature 2013) | Study: Breast Invasive Carcinoma (TCGA, Provosional) | GSEA-R Result Interpretation | Resolved limits | Linear Modeling of GSEA (GSEAlm) | Results interpretation: | Limitations: | Which Molecular Signature Data base (MSigDB) for gene list | get SubMSigDb for genes list | GSEAlm: Phenotypes into Disease | Disease Free Status (DFS_STATUS) into Prostate Cancer: | Copy Number Cluster Level into Stomach Adenocarcinoma: | GSEAlm: Disease vs Disease} | Breast vs Prostate Cancers: | Genes Classification using mRNA expression (Classification) | Genes vs Diseases (inter-diseases) | Example 1: Breast vs Glioblastoma vs Liver vs Lung Cancers (Figure~@ref(fig:GenesClass)A):} | Example 2: Bladder vs Breast vs Glioblastoma vs Lung vs Ovarian vs Prostate Cancers (Figure~\ref | Genes vs Phenotypes (intra-disease) | Example 1: Genes classification vs OS_STATUS (Living/Deceased) | Example 2: Genes regression vs OS_STATUS (Living/Deceased) | Example 3: Genes classification vs tumor grade (grade1/2/3) | Plots | Example: Association of P53 copy number alteration and mRNA exprssion in glioblastoma | Example: MAP2K2 and ABHD17A mRNA expression (RNA Seq V2 RSEM) levels in Uterine Corpus Endometrioid Carcinoma (TCGA, Nature 2013) | Survival Plots | Kaplan-Meier Curves | Cox proportional Hazards Model | Circos Style | References
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