TCGA BRCA RNA-seq Analysis

Data preparation

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  • Download data
  • Convert gene ID to Symbol format
  • Meta data information

PCA plot

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  • Create DEG object
  • PCA plots

Differentially Expressed Genes (DEG) analysis

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  • DEGs: Tumor vs Normal Tissue
  • Create DEG list
  • Volcanoplots
  • DEG table

GSEA

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  • GSEA with HALLMARK pathways
    • NES plot
    • Info table
  • GSEA with KEGG pathways
    • NES plot
    • Info table

ssGSEA

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  • HALLMARK pathways
  • KEGG pathways