1) TCGA Gene Expression Data ./tcga_get_manifest.py > tcga_manifest.txt ./tcga_get_files.py tcga_manifest.txt ./tcga_get_expressions.py tcga_manifest.txt output -o tcga_expr 2) LINCS - 3) ChemBL sqlite3 data/chembl/chembl_23/chembl_23_sqlite/chembl_23.db "SELECT DISTINCT md.molregno, md.chembl_id, act.standard_type, act.standard_value, act.standard_units FROM activities act, molecule_dictionary md WHERE act.molregno = MD.molregno AND act.standard_type = 'IC50'" | head 4) R Studio Proxy Setup emacs ~/.Renviron http_proxy = "http://proxy.swmed.edu:3128" https_proxy = "http://proxy.swmed.edu:3128" ftp_proxy = "proxy.swmed.edu:3128"