I am planning to conduct differential gene exression analysis on TCGA-COAD/READ samples. Currently the samples are ported to GDC portal and its difficult for me to handle.
My question is GDC portal shows ~ 600 samples for Colon under - data.category = "Transcriptome Profiling", data.type = "Gene expression quantification", workflow.type = "HTSeq - FPKM-UQ" . So how can i download these samples as a MATRIX file so that i can conduct Normal V/s Tumor comparison ?
Secondly How to download clinical data for the samples , every time .JASON file gets downloaded and i really don't know how to handle this. Please keep in mind i am not so good at programming/ IT skills and i am a biologist. I would appreciate if you can share a protocol on this. Thanks a lot for your support!!!