myTCGA

It's just a personal record for studying how to analysis TCGA data(expression+mutation+methylation+CNV)

expression

mRNA

GSE62944

I donwload the expression matrix from GEO

• GSE62944_01_27_15_TCGA_20_420_Clinical_Variables_7706_Samples.txt.gz
• GSE62944_01_27_15_TCGA_20_CancerType_Samples.txt.gz
• GSE62944_06_01_15_TCGA_24_548_Clinical_Variables_9264_Samples.txt.gz
• GSE62944_06_01_15_TCGA_24_CancerType_Samples.txt.gz
• GSE62944_06_01_15_TCGA_24_Normal_CancerType_Samples.txt.gz
• GSM1536837_06_01_15_TCGA_24.tumor_Rsubread_FPKM.txt.gz
• GSM1697009_06_01_15_TCGA_24.normal_Rsubread_FPKM.txt.gz

Then load these file into mysql by using R package(I'm not familar with SQL, so I choose R)

TODO

miRNA

TODO

protaion

TODO

mutation

TODO

CNV

TODO

methylation

TODO

combination

TODO

cbioportal(cgdsR)