merge pipelines and clean up

cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium

https://cumc.github.io/xqtl-protocol/

MIT License

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merge pipelines and clean up #1066

Closed Chunmingl closed 2 months ago

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gaow commented 2 months ago

@Chunmingl this file code/pecotmr_integration/python.ipynb is it necessary? Please remove it if not.

Chunmingl commented 2 months ago

This file code/pecotmr_integration/python.ipynb is removed

gaow commented 2 months ago

okay for ctwas the codes are also all commented out. I think at this point we should try to test the cTWAS codes and see if it works? Also does ctwas really depends on sos_variable(regional_data) because i have not seen it used?

Chunmingl commented 2 months ago

the sos variables were updated after testing on twas and ctwas pipelines together