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PayamDiba / SERGIO

A simulator for single-cell expression data guided by gene regulatory networks
GNU General Public License v3.0
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Where to get my own GRN as input? #5

Closed qianxu05172019 closed 4 years ago

qianxu05172019 commented 4 years ago

Hi,

I am wondering where I can download or generate the GRN file for a specific cell type as the input file for SERGIO?

PayamDiba commented 4 years ago

If you do not have a particular GRN, you can always use the sample GRNs that we provided in "data_sets" folder.

But, if you have a particular GRN structure that want to simulate you can easily convert it to input files suitable for SERGIO. All you need to do is to convert it into a proper format that SERGIO expects for "input_file_taregts" (please see README to find this file format). You also need to find the master regulators (MR) in your GRN and prepare a "input_file_regs" file that has one row for each MR and columns showing production rates in different cell-types (please see README).

We understand that users might like to use their own GRN structure and hypothetical cell-types compositions and it requires a converter that automatically prepares SERGIO's input file from user files. We apologize for not having such a functionality at the moment but we will work on this in the near future.

qianxu05172019 commented 4 years ago

Got you. thanks for your reply!