TCGA data downloaded from GDC

Question

[datanerd]

HI guys,

I have downloaded a bunch pf projects from the TCGA data using the GDC client. I have a manifest files that I combined with the sample file and every file has an associated folder with the id. I was looking for ideas how to best query this data to select the subset of files I want. Many of the R/python packages support data query directly through the GDC API. However, I was thinking of querying on the set of data set using the metadata file (manifest with sample info) downloaded from GDC sitting locally. Would appreciate any advice or ideas on how to best approach this.

Thanks, Mamta