Signatures calculation procedure

[aurbn]

Hello!

Thank you for the great resource!

I have tried to, but didn't manage to find the procedure for calculating scores—those in the section "Computed Signatures for CycleGAN Predicted RNA-Seq-Like Profiles of L1000 Samples (Level 5)." As I understand, it uses the "Characteristic Direction" method. For my project, I need fold changes along with p-values for reconstructed RNA-seq data. Especially, I am interested in how to match experimental samples and controls to produce case-control groups. Is this code present somewhere?

[AviMaayan]

Hi @aurbn,

You can find more information about the procedure in this paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04895-5

The code is available from this repo:
https://github.com/MaayanLab/L1000toRNAseq

Best,

Avi