Running DepRanker in command line mode:
From the source(src) directory of DepRanker, the main script can be executed on the test dataset provided with the package as follows:
cd deprankergui-git
python3 depranker.py -roast datafile/run2/AWScreen2_roast.csv -toptags datafile/run2/AWScreen2_toptags.csv -exprs datafile/run2/geneexp.csv -cnv datafile/run2/copynumber.csv -out datafile/run2/ouput_rank.txt
optional arguments:
-h, --help show this help message and exit
-roast ROAST_RESULT_FILE
-toptags EDGER_TOPTAGS_FILE
-exprs EXPRESSION_FILE
-cnv COPY_NUMBER_VARIATION_FILE
-out OUTPUT_FILE Ouput file
-min_shrna MINGENES Minimum number of shRNA representation (integer)
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