polish cellsigDB (the minimum standard)

stemangiola / cellsig

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polish cellsigDB (the minimum standard) #49

Closed stemangiola closed 1 year ago

stemangiola commented 2 years ago

todos:

Execute as sanity check this file https://github.com/stemangiola/cellsig/blob/Kamran/dev/process_counts.R and make sure you can reconstruct the raw caounts
If you did add more raw data, create a new R script called parse_fourth_databse.R
Add the call to parse_fourth_databse.R to process_counts.R and re execute process counts to see that you get the raw data back
polish any of the parse_*_databse.R when you find mistakes (JUST THE BIG ONES)

Kamran-Khan96 commented 2 years ago

Hi @stemangiola ,

Apologies for the late response.

It seems in the the source files of the raw counts aren't in the git repository yet. Particularly, the source file for calling the functions in aren't even specified in parse_second_database.R and parse_third_database.R. Maybe I'm understanding it wrong.

I'll just try to pinpoint the major issues (if there's any) rather than going very deep into the matter.

stemangiola commented 2 years ago

It seems in the the source files of the raw counts aren't in the git repository yet.

When you are in the WEHI server I will share the database directory with you.

Particularly, the source file for calling the functions in aren't even specified in parse_second_database.R and parse_third_database.R. Maybe I'm understanding it wrong.

I'm trying to understand this. I have asked access to Jian directory at WEHI, I will try to find those files there

Kamran-Khan96 commented 1 year ago

Resolved