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stjude / cis-x

Search for activating regulatory variants in the tumor genome
https://www.stjuderesearch.org/site/lab/zhang/cis-x
Apache License 2.0
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New updates from Yu, #10

Closed xiaolongchen0627 closed 3 years ago

xiaolongchen0627 commented 3 years ago

"collect.cohort.pl” -> src/ref-exp/src “cis-X-ref-exp-preprocess” -> src/ref-exp/bin

zaeleus commented 3 years ago

Do you have example input for running ref-exp? This is not included in the demo dataset.

Also, can you describe what columns 19 and 22 are in the preprocessed expression matrix ($expfile) and why they changed from columns 17 and 20?

xiaolongchen0627 commented 3 years ago

Yes, I can send you a example for runing ref-exp. And the columns 17 is actually a serious mistake that should be corrected . And he now use a fdr in column 22 to replace a previous pvalue in column 20