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Currently, if a user wants to use GenePlexus with their custom network or gsc, they will need to set up the required custom files using the geneplexus.custom module first, before they can proceed to run the GenePlexus pipeline using the CLI.
The goal here is to make a CLI option that calls the necessary geneplexus.custom functions to set up custom files, and thus eliminates the need for one to manually prepare them.
Working notes
--custom option -> enables preprocessing custom network/gsc data
Preprocessing runlong also save to ${data_dir}/custom_logs/${net}_${feature}_${gsc}.log
Currently, if a user wants to use GenePlexus with their custom network or gsc, they will need to set up the required custom files using the
geneplexus.custom
module first, before they can proceed to run the GenePlexus pipeline using the CLI.The goal here is to make a CLI option that calls the necessary
geneplexus.custom
functions to set up custom files, and thus eliminates the need for one to manually prepare them.Working notes
--custom
option -> enables preprocessing custom network/gsc data${data_dir}/custom_logs/${net}_${feature}_${gsc}.log
num_nodes
,num_edges
num_genesets
,med_size
,avg_size
,std_size
,max_size
,min_size
Edgelist_xxx.edg
(custom network)GSCOriginal_xxx.json
(custom gsc)custom.edgelist_to_node
->NodeOrder_${net}.txt
custom.edgelist_to_matrix
->Data_${feature}_{network}.npy
custom.subset_gsc_to_network
->GSC_${gsc}_${net}_GoodSets.json
,GSC_${gsc}_${net}_universe.txt
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