GitHub - infphilo/cowork

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Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
data		data
Alluri_Kim_GSE12790_20180227.html		Alluri_Kim_GSE12790_20180227.html
Finn_2009.txt		Finn_2009.txt
GSE12790.Rmd		GSE12790.Rmd
GSE12790_series_matrix.txt.gz		GSE12790_series_matrix.txt.gz
README		README
bibliography.bib		bibliography.bib
calculate_tcga_gene_expr.R		calculate_tcga_gene_expr.R
lincs_cell_info.csv		lincs_cell_info.csv
lincs_cell_line_weight.csv		lincs_cell_line_weight.csv
lincs_landmark.csv		lincs_landmark.csv
lincs_sig_info.csv		lincs_sig_info.csv
tcga_get_expressions.py		tcga_get_expressions.py
tcga_get_files.py		tcga_get_files.py
tcga_get_manifest.py		tcga_get_manifest.py

Repository files navigation

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"