jyyulab / dasatinib-tall Goto Github PK

Thanks for your excellent work! I am trying to apply your 30 biomarker score and driver gene activity modules on my T-ALL expression data, and I've read your code and paper carefully, it seems I still need some files (TARGET_TALL_merge.network.RData , Discovery_msTable.xlsx, and preTCR_dasatinib_Targets) to calculate the score and activity. I'll be grateful if you would like to share your output file, but I can totally understand if those data are under-protected.

To calculate driver activity, the TARGET TALL network ./SJAR/TARGET_TALL_merge.network.RData (source code) is the key file, and its upstream input file is sig_tf <- read.xlsx("SIG_TF_list.xlsx") (source code). I'm wondering if the same file between "SIG_TF_list.xlsx" and the default SIG and TF list in NetBID2 package?

To calculate 30 biomarker score in 3.1.get30biomarker_score.R, I think ./DATA/Discovery/Discovery_msTable.xlsx (source code) and ./DATA/combined/preTCR_dasatinib_Targets (no source code found) are necessary. I've checked the paper supplement data and only find some information at SourceData_Fig3C about preTCR_dasatinib_Targets, but I don't know if the list in source data is complete.

Thanks again and looking forward to your reply~
Best wishes
Bowen
[email protected]